diff --git a/covid_comp_script0_table.Rnw b/covid_comp_script0_table.Rnw
index 7243ad4eb56975729ac69194a134b2bb9983bc29..4ee4905dd07fdbc0960a4d2b2e5605bc46338869 100644
--- a/covid_comp_script0_table.Rnw
+++ b/covid_comp_script0_table.Rnw
@@ -128,10 +128,33 @@ names(dginnT)<-c("File", "Name", "Gene.name", "GeneSize",
"dginn-primate_codemlM7M8.PSS")
@
+<<eval=FALSE>>=
+table(dginnT$`dginn-primate_BUSTED`)
+table(dginnT$`dginn-primate_codemlM1M2`)
+table(dginnT$`dginn-primate_codemlM7M8`)
+table(dginnT$`dginn-primate_BppM1M2`)
+table(dginnT$`dginn-primate_BppM7M8`)
+
+table(dginnT$`dginn-primate_BUSTED`=="na",dginnT$`dginn-primate_codemlM1M2`=="na", dginnT$`dginn-primate_codemlM7M8`=="na",
+ dginnT$`dginn-primate_BppM1M2`=="na", dginnT$`dginn-primate_BppM7M8`=="na" )
+
+@
+
+
+
\subsection{Join Table and DGINN table}
<<>>=
tab<-merge(tab,dginnT, by="Gene.name", all.x=T)
+
+table(tab$`dginn-primate_BUSTED`)
+table(tab$`dginn-primate_codemlM1M2`)
+table(tab$`dginn-primate_codemlM7M8`)
+table(tab$`dginn-primate_BppM1M2`)
+table(tab$`dginn-primate_BppM7M8`)
+table(tab$`dginn-primate_BUSTED`=="na" | tab$`dginn-primate_codemlM1M2`=="na" | tab$`dginn-primate_codemlM7M8`=="na" |
+ tab$`dginn-primate_BppM1M2`=="na"| tab$`dginn-primate_BppM7M8`=="na" )
+
@
\subsection{Add DGINN results on bat dataset}
@@ -153,7 +176,6 @@ dginnbatsnew2<-read.delim(paste0(workdir,
fill=T, h=T)
# colomne choice, BUSTED and Bppml form first file, codeml from the other one
-
dginnbatsnew<-dginnbatsnew1
dginnbatsnew$omegaM0codeml<-dginnbatsnew2$omegaM0codeml
@@ -245,5 +267,219 @@ tab<-merge(tab,dginnbats, by="cooper.batsGene", all.x=T)
write.table(tab, "covid_comp_complete.txt", row.names=FALSE, quote=FALSE, sep="\t")
@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+\section{Second Table}
+
+Table containing the DGINN results for both Primates and bats. Conserve all genes.
+
+\subsection{Primates}
+
+<<>>=
+dginnT<-read.delim(paste0(workdir,
+ "data/DGINN_202005281649summary_cleaned.csv"),
+ fill=T, h=T, sep=",")
+
+dim(dginnT)
+names(dginnT)
+
+# Rename the columns to include primate
+names(dginnT)<-c("File", "Name", "Gene.name", "GeneSize",
+ "dginn-primate_NbSpecies", "dginn-primate_omegaM0Bpp",
+ "dginn-primate_omegaM0codeml", "dginn-primate_BUSTED",
+ "dginn-primate_BUSTED.p.value", "dginn-primate_MEME.NbSites",
+ "dginn-primate_MEME.PSS", "dginn-primate_BppM1M2",
+ "dginn-primate_BppM1M2.p.value", "dginn-primate_BppM1M2.NbSites",
+ "dginn-primate_BppM1M2.PSS", "dginn-primate_BppM7M8",
+ "dginn-primate_BppM7M8.p.value", "dginn-primate_BppM7M8.NbSites",
+ "dginn-primate_BppM7M8.PSS", "dginn-primate_codemlM1M2",
+ "dginn-primate_codemlM1M2.p.value", "dginn-primate_codemlM1M2.NbSites",
+ "dginn-primate_codemlM1M2.PSS", "dginn-primate_codemlM7M8",
+ "dginn-primate_codemlM7M8.p.value", "dginn-primate_codemlM7M8.NbSites",
+ "dginn-primate_codemlM7M8.PSS")
+@
+
+\subsection{Bats}
+
+<<>>=
+# original table
+dginnbats<-read.delim(paste0(workdir,
+ "data/DGINN_202005281339summary_cleaned-LE201108.txt"),
+ fill=T, h=T)
+
+# rerun on corrected alignment
+dginnbatsnew<-read.delim(paste0(workdir,
+ "data/DGINN_202011262248_hyphybpp-202012192053_codeml-summary.txt"),
+ fill=T, h=T)
+
+@
+<<>>=
+# Add both columns
+dginnbatsnew$Lucie.s.comments<-""
+dginnbatsnew$Action.taken<-""
+
+# Homogenize column names
+dginnbats$BUSTED_p.value<-dginnbats$BUSTED.p.value
+dginnbats$MEME_NbSites<-dginnbats$MEME.NbSites
+dginnbats$MEME_PSS<-dginnbats$MEME.PSS
+
+dginnbats$BppM1M2_p.value<-dginnbats$BppM1M2.p.value
+dginnbats$BppM1M2_NbSites<-dginnbats$BppM1M2.NbSites
+dginnbats$BppM1M2_PSS<-dginnbats$BppM1M2.PSS
+
+dginnbats$BppM7M8_p.value<-dginnbats$BppM7M8.p.value
+dginnbats$BppM7M8_NbSites<-dginnbats$BppM7M8.NbSites
+dginnbats$BppM7M8_PSS<-dginnbats$BppM7M8.PSS
+
+dginnbats$codemlM1M2_p.value<-dginnbats$codemlM1M2.p.value
+dginnbats$codemlM1M2_NbSites<-dginnbats$codemlM1M2.NbSites
+dginnbats$codemlM1M2_PSS<-dginnbats$codemlM1M2.PSS
+
+dginnbats$codemlM7M8_p.value<-dginnbats$codemlM7M8.p.value
+dginnbats$codemlM7M8_NbSites<-dginnbats$codemlM7M8.NbSites
+dginnbats$codemlM7M8_PSS<-dginnbats$codemlM7M8.PSS
+@
+
+<<>>=
+# Order columns in the same order in both tables
+dginnbats<-dginnbats[,names(dginnbatsnew)]
+
+names(dginnbatsnew) %in% names(dginnbats)
+names(dginnbats)==names(dginnbatsnew)
+
+# Put RIPK aside
+ripk1<-dginnbatsnew[dginnbatsnew$Gene=="RIPK1",1:27]
+
+# Add it to primate table
+names(ripk1)<-names(dginnT)
+
+ripk1$`dginn-primate_omegaM0Bpp`<-as.factor(ripk1$`dginn-primate_omegaM0Bpp`)
+ripk1$`dginn-primate_BUSTED.p.value`<-as.factor(ripk1$`dginn-primate_BUSTED.p.value`)
+ripk1$`dginn-primate_BppM1M2.p.value`<-as.factor(ripk1$`dginn-primate_BppM1M2.p.value`)
+ripk1$`dginn-primate_BppM7M8.p.value`<-as.factor(ripk1$`dginn-primate_BppM7M8.p.value`)
+
+dginnT<-rbind(dginnT, ripk1)
+
+## Remove it Ripk1 from bats
+dginnbatsnew<-dginnbatsnew[dginnbatsnew$Gene!="RIPK1",]
+
+
+## suppress redundant lines
+dginnbats<-dginnbats[(dginnbats$Gene %in% dginnbatsnew$Gene)==FALSE,]
+names(dginnbatsnew)<-names(dginnbats)
+
+## replace by new data
+dginnbatsnew$omegaM0Bpp<-as.factor(dginnbatsnew$omegaM0Bpp)
+dginnbatsnew$BppM1M2_p.value<-as.factor(dginnbatsnew$BppM1M2_p.value)
+dginnbatsnew$BppM7M8_p.value<-as.factor(dginnbatsnew$BppM7M8_p.value)
+
+dginnbats<-rbind(dginnbats, dginnbatsnew)
+
+names(dginnbats)<-c("bats_File", "bats_Name", "Gene.name", paste0("bats_",
+ names(dginnbats)[-(1:3)]))
+names(dginnbats)
+
+@
+
+\subsection{Merged table}
+<<setup, include=FALSE, cache=FALSE, tidy=TRUE>>=
+options(tidy=TRUE, width=70)
+@
+<<>>=
+#tidy.opts = list(width.cutoff = 60)
+dim(dginnT)
+dginnT$Gene.name
+dim(dginnbats)
+dginnbats$Gene.name
+@
+
+Manual corrections:
+
+TMPRSS2 in bats
+<<>>=
+dginnbats[dginnbats$Gene.name=="TMPRSS2",]
+# keeping the uncut one
+# renaming the other one TMPRSS2_cut
+dginnbats[dginnbats$bats_File=="TMPRSS2_bat_select_cut_mafft_prank","Gene.name"]<-"TMPRSS2_cut"
+@
+
+RIPK1: ANcestral version kept, suppress it "RIPK1\_sequences\_filtered\_longestORFs\_mafft\_mincov\_prank"
+<<>>=
+dginnT<-dginnT[dginnT$File!="RIPK1_sequences_filtered_longestORFs_mafft_mincov_prank",]
+@
+
+REEP6 eA et B
+<<>>=
+dginnbats$Gene.name<-as.character(dginnbats$Gene.name)
+dginnbats[dginnbats$bats_File=="REEP6_sequences_filtered_longestORFs_D210gp1_prank", "Gene.name"]<-"REEP6_old"
+dginnbats[dginnbats$bats_File=="REEP6_LA_bat_select_mafft_prank", "Gene.name"]<-"REEP6"
+dginnbats[dginnbats$bats_File=="REEP6_LB_bat_select_mafft_prank", "Gene.name"]<-"REEP6_like"
+@
+
+GNG5
+<<>>=
+dginnT$Gene.name<-as.character(dginnT$Gene.name)
+dginnT[dginnT$File=="GNG5_sequences_filtered_longestORFs_D189gp2_prank", "Gene.name"]<-"GNG5_like"
+@
+
+
+<<>>=
+dim(dginnbats)
+dim(dginnT)
+
+# genes in common
+dginnT$Gene.name[dginnT$Gene.name %in% dginnbats$Gene.name]
+length(dginnT$Gene.name[dginnT$Gene.name %in% dginnbats$Gene.name])
+
+# genes only in primates
+dginnT$Gene.name[(dginnT$Gene.name %in% dginnbats$Gene.name)==FALSE]
+length(dginnT$Gene.name[(dginnT$Gene.name %in% dginnbats$Gene.name)==FALSE])
+
+# genes only in bats
+dginnbats$Gene.name[(dginnbats$Gene.name %in% dginnT$Gene.name)==FALSE]
+length(dginnbats$Gene.name[(dginnbats$Gene.name %in% dginnT$Gene.name)==FALSE])
+
+@
+
+<<>>=
+tab<-merge(dginnT, dginnbats, by="Gene.name", all.x=T, all.y=T)
+dim(tab)
+
+write.table(tab, "covid_comp_alldginn.txt", sep="\t")
+@
+
+
\end{document}
diff --git a/covid_comp_script0_table.html b/covid_comp_script0_table.html
new file mode 100644
index 0000000000000000000000000000000000000000..9424673c2bfd4e92c740dffd071b29499aeee09d
--- /dev/null
+++ b/covid_comp_script0_table.html
@@ -0,0 +1,3439 @@
+<!DOCTYPE html>
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+
+<title>[1] 332 84</title>
+
+<script type="text/javascript">
+window.onload = function() {
+ var imgs = document.getElementsByTagName('img'), i, img;
+ for (i = 0; i < imgs.length; i++) {
+ img = imgs[i];
+ // center an image if it is the only element of its parent
+ if (img.parentElement.childElementCount === 1)
+ img.parentElement.style.textAlign = 'center';
+ }
+};
+</script>
+
+
+
+<!-- MathJax scripts -->
+<script type="text/javascript" src="https://cdn.bootcss.com/mathjax/2.7.0/MathJax.js?config=TeX-MML-AM_CHTML">
+</script>
+
+
+<style type="text/css">
+body, td {
+ font-family: sans-serif;
+ background-color: white;
+ font-size: 13px;
+}
+
+body {
+ max-width: 800px;
+ margin: auto;
+ padding: 1em;
+ line-height: 20px;
+}
+
+tt, code, pre {
+ font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace;
+}
+
+h1 {
+ font-size:2.2em;
+}
+
+h2 {
+ font-size:1.8em;
+}
+
+h3 {
+ font-size:1.4em;
+}
+
+h4 {
+ font-size:1.0em;
+}
+
+h5 {
+ font-size:0.9em;
+}
+
+h6 {
+ font-size:0.8em;
+}
+
+a:visited {
+ color: rgb(50%, 0%, 50%);
+}
+
+pre, img {
+ max-width: 100%;
+}
+pre {
+ overflow-x: auto;
+}
+pre code {
+ display: block; padding: 0.5em;
+}
+
+code {
+ font-size: 92%;
+ border: 1px solid #ccc;
+}
+
+code[class] {
+ background-color: #F8F8F8;
+}
+
+table, td, th {
+ border: none;
+}
+
+blockquote {
+ color:#666666;
+ margin:0;
+ padding-left: 1em;
+ border-left: 0.5em #EEE solid;
+}
+
+hr {
+ height: 0px;
+ border-bottom: none;
+ border-top-width: thin;
+ border-top-style: dotted;
+ border-top-color: #999999;
+}
+
+@media print {
+ * {
+ background: transparent !important;
+ color: black !important;
+ filter:none !important;
+ -ms-filter: none !important;
+ }
+
+ body {
+ font-size:12pt;
+ max-width:100%;
+ }
+
+ a, a:visited {
+ text-decoration: underline;
+ }
+
+ hr {
+ visibility: hidden;
+ page-break-before: always;
+ }
+
+ pre, blockquote {
+ padding-right: 1em;
+ page-break-inside: avoid;
+ }
+
+ tr, img {
+ page-break-inside: avoid;
+ }
+
+ img {
+ max-width: 100% !important;
+ }
+
+ @page :left {
+ margin: 15mm 20mm 15mm 10mm;
+ }
+
+ @page :right {
+ margin: 15mm 10mm 15mm 20mm;
+ }
+
+ p, h2, h3 {
+ orphans: 3; widows: 3;
+ }
+
+ h2, h3 {
+ page-break-after: avoid;
+ }
+}
+</style>
+
+
+
+</head>
+
+<body>
+<p>\documentclass[11pt, oneside]{article}\usepackage[]{graphicx}\usepackage[]{color}
+% maxwidth is the original width if it is less than linewidth
+% otherwise use linewidth (to make sure the graphics do not exceed the margin)
+\makeatletter
+\def\maxwidth{ %
+ \ifdim\Gin@nat@width>\linewidth
+ \linewidth
+ \else
+ \Gin@nat@width
+ \fi
+}
+\makeatother</p>
+
+<p>\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
+\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
+\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
+\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
+\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
+\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
+\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
+\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
+\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
+\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
+\let\hlipl\hlkwb</p>
+
+<p>\usepackage{framed}
+\makeatletter
+\newenvironment{kframe}{%
+ \def\at@end@of@kframe{}%
+ \ifinner\ifhmode%
+ \def\at@end@of@kframe{\end{minipage}}%
+ \begin{minipage}{\columnwidth}%
+ \fi\fi%
+ \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
+ \colorbox{shadecolor}{##1}\hskip-\fboxsep
+ % There is no \@totalrightmargin, so:
+ \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
+ \MakeFramed {\advance\hsize-\width
+ \@totalleftmargin\z@ \linewidth\hsize
+ \@setminipage}}%
+ {\par\unskip\endMakeFramed%
+ \at@end@of@kframe}
+\makeatother</p>
+
+<p>\definecolor{shadecolor}{rgb}{.97, .97, .97}
+\definecolor{messagecolor}{rgb}{0, 0, 0}
+\definecolor{warningcolor}{rgb}{1, 0, 1}
+\definecolor{errorcolor}{rgb}{1, 0, 0}
+\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX</p>
+
+<p>\usepackage{alltt} % use “amsart” instead of “article” for AMSLaTeX format
+%\usepackage{geometry} % See geometry.pdf to learn the layout options. There are lots.
+%\geometry{letterpaper} % … or a4paper or a5paper or …
+%\geometry{landscape} % Activate for for rotated page geometry
+%\usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
+%\usepackage{graphicx} % Use pdf, png, jpg, or eps with pdflatex; use eps in DVI mode
+ % TeX will automatically convert eps –> pdf in pdflatex<br/>
+%\usepackage{amssymb}</p>
+
+<p>\usepackage[utf8]{inputenc}
+%\usepackage[cyr]{aeguill}
+%\usepackage[francais]{babel}
+%\usepackage{hyperref}</p>
+
+<p>\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
+\author{Marie Cariou}
+\date{Janvier 2021} % Activate to display a given date or no date
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\begin{document}
+\maketitle</p>
+
+<p>\tableofcontents</p>
+
+<p>\newpage</p>
+
+<p>\section{Files manipulations}</p>
+
+<p>\subsection{Read Janet Young's table}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{workdir}\hlkwb{<-}\hlstr{“/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/”}</p>
+
+<p>\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{“data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv”}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{dec}\hlstd{=}\hlstr{“,”}\hlstd{)}
+\hlkwd{dim}\hlstd{(tab)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 332 84</h2>
+
+<p>\end{verbatim}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\subsection{Read DGINN Young table}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnY}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{“data/summary_primate_young.res”}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}</p>
+
+<p>\hlkwd{dim}\hlstd{(dginnY)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 1992 7</h2>
+
+<p>\end{verbatim}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\subsection{Joining Young and DGINN Young table}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# correct gene names (MARC1)}
+\hlstd{val_remp}\hlkwb{=}\hlkwd{as.character}\hlstd{(}\hlkwd{unique}\hlstd{(dginnY}\hlopt{\(}\hlstd{Gene)[(}\hlkwd{unique}\hlstd{(dginnY}\hlopt{\)}\hlstd{Gene)} \hlopt{%in%}
+ \hlstd{tab}\hlopt{\(}\hlstd{Gene.name)}\hlopt{==}\hlstd{F])}
+\hlstd{tab}\hlopt{\)}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{\(}\hlstd{Gene.name)}
+\hlstd{tab}\hlopt{\)}\hlstd{Gene.name[}\hlnum{158}\hlstd{]}\hlkwb{<-}\hlstd{val_remp}
+\hlkwd{sum}\hlstd{(}\hlkwd{unique}\hlstd{(dginnY}\hlopt{\(}\hlstd{Gene)} \hlopt{%in%} \hlkwd{unique}\hlstd{(tab}\hlopt{\)}\hlstd{Gene.name))}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 332</h2>
+
+<p>\end{verbatim}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{add_col}\hlkwb{<-}\hlkwa{function}\hlstd{(}\hlkwc{method}\hlstd{=}\hlstr{“PamlM1M2”}\hlstd{){}</p>
+
+<p>\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstd{method,}
+ \hlkwd{c}\hlstd{(}\hlstr{“Gene”}\hlstd{,} \hlstr{“Omega”}\hlstd{,} \hlstr{“PosSel”}\hlstd{,} \hlstr{“PValue”}\hlstd{,} \hlstr{“NbSites”}\hlstd{,} \hlstr{“PSS”}\hlstd{)]}</p>
+
+<p>\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“Gene.name”}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{“Omega<em>”}\hlstd{, method),}
+ \hlkwd{paste0}\hlstd{(}\hlstr{“PosSel</em>”}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{“PValue<em>”}\hlstd{, method),}
+ \hlkwd{paste0}\hlstd{(}\hlstr{“NbSites</em>”}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{“PSS_”}\hlstd{, method))}</p>
+
+<p>\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{“Gene.name”}\hlstd{)}</p>
+
+<p>\hlkwd{return}\hlstd{(tab)}
+\hlstd{}}</p>
+
+<p>\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{“PamlM1M2”}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{“PamlM7M8”}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{“BppM1M2”}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{“BppM7M8”}\hlstd{)}</p>
+
+<p>\hlcom{# Manip pour la colonne BUSTED}</p>
+
+<p>\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{“BUSTED”}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{“Gene”}\hlstd{,} \hlstr{“Omega”}\hlstd{,} \hlstr{“PosSel”}\hlstd{,} \hlstr{“PValue”}\hlstd{)]}
+\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“Gene.name”}\hlstd{,} \hlstr{“Omega_BUSTED”}\hlstd{,} \hlstr{“PosSel_BUSTED”}\hlstd{,} \hlstr{“PValue_BUSTED”}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{“Gene.name”}\hlstd{)}</p>
+
+<p>\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{“MEME”}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{“Gene”}\hlstd{,} \hlstr{“NbSites”}\hlstd{,} \hlstr{“PSS”}\hlstd{)]}
+\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“Gene.name”}\hlstd{,} \hlstr{“NbSites_MEME”}\hlstd{,} \hlstr{“PSS_MEME”}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{“Gene.name”}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\subsection{Read DGINN Table}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnT}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{“data/DGINN_202005281649summary_cleaned.csv”}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{“,”}\hlstd{)}</p>
+
+<p>\hlkwd{dim}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 412 27</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{names}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] “File”</h2>
+
+<h2>[2] “Name”</h2>
+
+<h2>[3] “Gene”</h2>
+
+<h2>[4] “GeneSize”</h2>
+
+<h2>[5] “NbSpecies”</h2>
+
+<h2>[6] “omegaM0Bpp”</h2>
+
+<h2>[7] “omegaM0codeml”</h2>
+
+<h2>[8] “BUSTED”</h2>
+
+<h2>[9] “BUSTED.p.value”</h2>
+
+<h2>[10] “MEME.NbSites”</h2>
+
+<h2>[11] “MEME.PSS”</h2>
+
+<h2>[12] “BppM1M2”</h2>
+
+<h2>[13] “BppM1M2.p.value”</h2>
+
+<h2>[14] “BppM1M2.NbSites”</h2>
+
+<h2>[15] “BppM1M2.PSS”</h2>
+
+<h2>[16] “BppM7M8”</h2>
+
+<h2>[17] “BppM7M8.p.value”</h2>
+
+<h2>[18] “BppM7M8.NbSites”</h2>
+
+<h2>[19] “BppM7M8.PSS”</h2>
+
+<h2>[20] “codemlM1M2”</h2>
+
+<h2>[21] “codemlM1M2.p.value”</h2>
+
+<h2>[22] “codemlM1M2.NbSites”</h2>
+
+<h2>[23] “codemlM1M2.PSS”</h2>
+
+<h2>[24] “codemlM7M8”</h2>
+
+<h2>[25] “codemlM7M8.p.value”</h2>
+
+<h2>[26] “codemlM7M8.NbSites”</h2>
+
+<h2>[27] “codemlM7M8.PSS”</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlcom{# Number of genes in dginn-primate output not present in the original table}
+\hlstd{dginnT[(dginnT}\hlopt{\(}\hlstd{Gene} \hlopt{%in%} \hlstd{tab}\hlopt{\)}\hlstd{Gene.name)}\hlopt{==}\hlstd{F,}\hlstr{“Gene”}\hlstd{]}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] ACE2</h2>
+
+<h2>[2] ADAM9[0-3120]</h2>
+
+<h2>[3] ADAM9[3119-3927]</h2>
+
+<h2>[4] ATP5MGL</h2>
+
+<h2>[5] C1H1ORF50</h2>
+
+<h2>[6] CEP135[0-3264]</h2>
+
+<h2>[7] CEP135[3263-3678]</h2>
+
+<h2>[8] CEP43</h2>
+
+<h2>[9] COQ8B</h2>
+
+<h2>[10] COQ8A</h2>
+
+<h2>[11] CSNK2A1</h2>
+
+<h2>[12] CSNK2B[0-609]</h2>
+
+<h2>[13] CSNK2B[608-2568]</h2>
+
+<h2>[14] CYB5R1</h2>
+
+<h2>[15] DDX21[0-717]</h2>
+
+<h2>[16] DDX21[716-2538]</h2>
+
+<h2>[17] DDX50</h2>
+
+<h2>[18] DNAJC15</h2>
+
+<h2>[19] DPH5[0-702]</h2>
+
+<h2>[20] DPH5[701-1326]</h2>
+
+<h2>[21] DPY19L2</h2>
+
+<h2>[22] ELOC</h2>
+
+<h2>[23] ERO1B</h2>
+
+<h2>[24] EXOSC3[0-1446]</h2>
+
+<h2>[25] EXOSC3[1445-1980]</h2>
+
+<h2>[26] FBN3</h2>
+
+<h2>[27] GNB4</h2>
+
+<h2>[28] GNB2</h2>
+
+<h2>[29] GNB3</h2>
+
+<h2>[30] GOLGA7[0-312]</h2>
+
+<h2>[31] GOLGA7[311-549]</h2>
+
+<h2>[32] GPX1[0-1218]</h2>
+
+<h2>[33] GPX1[1217-2946]</h2>
+
+<h2>[34] HDAC1</h2>
+
+<h2>[35] HS6ST3</h2>
+
+<h2>[36] IMPDH1</h2>
+
+<h2>[37] ITGB1[0-2328]</h2>
+
+<h2>[38] ITGB1[2327-2844]</h2>
+
+<h2>[39] LMAN2L</h2>
+
+<h2>[40] MRPS5[0-1569]</h2>
+
+<h2>[41] MRPS5[1568-3783]</h2>
+
+<h2>[42] MARC2</h2>
+
+<h2>[43] MGRN1</h2>
+
+<h2>[44] NDFIP2[0-768]</h2>
+
+<h2>[45] NDFIP2[767-1314]</h2>
+
+<h2>[46] NDUFAF2[0-258]</h2>
+
+<h2>[47] NDUFAF2[257-744]</h2>
+
+<h2>[48] NSD2</h2>
+
+<h2>[49] NUP58</h2>
+
+<h2>[50] NUP58[0-1824]</h2>
+
+<h2>[51] NUP58[1823-2367]</h2>
+
+<h2>[52] PABPC3</h2>
+
+<h2>[53] POTPABPC1</h2>
+
+<h2>[54] PABPC4L</h2>
+
+<h2>[55] PABPC5</h2>
+
+<h2>[56] PCSK5</h2>
+
+<h2>[57] PRIM2[0-1071]</h2>
+
+<h2>[58] PRIM2[1070-1902]</h2>
+
+<h2>[59] PRKACB</h2>
+
+<h2>[60] PRKACG</h2>
+
+<h2>[61] PTGES2[0-1587]</h2>
+
+<h2>[62] PTGES2[1586-2202]</h2>
+
+<h2>[63] RAB8B</h2>
+
+<h2>[64] RAB13</h2>
+
+<h2>[65] RAB18[0-855]</h2>
+
+<h2>[66] RAB18[854-1815]</h2>
+
+<h2>[67] RAB2B</h2>
+
+<h2>[68] RAB5A</h2>
+
+<h2>[69] RAB5B</h2>
+
+<h2>[70] RAB15</h2>
+
+<h2>[71] RALB</h2>
+
+<h2>[72] EZR</h2>
+
+<h2>[73] EZR[0-1458]</h2>
+
+<h2>[74] EZR[1457-3771]</h2>
+
+<h2>[75] MSN</h2>
+
+<h2>[76] RETREG3</h2>
+
+<h2>[77] RHOB</h2>
+
+<h2>[78] RHOC</h2>
+
+<h2>[79] SLC44A2[0-2577]</h2>
+
+<h2>[80] SLC44A2[2576-3657]</h2>
+
+<h2>[81] SPART</h2>
+
+<h2>[82] SRP72[0-2604]</h2>
+
+<h2>[83] SRP72[2603-3417]</h2>
+
+<h2>[84] STOM[0-1047]</h2>
+
+<h2>[85] STOM[1046-1800]</h2>
+
+<h2>[86] STOML3</h2>
+
+<h2>[87] TIMM29</h2>
+
+<h2>[88] TLE4</h2>
+
+<h2>[89] TLE2</h2>
+
+<h2>[90] TLE2[0-1302]</h2>
+
+<h2>[91] TLE2[1301-3987]</h2>
+
+<h2>[92] TMPRSS2</h2>
+
+<h2>[93] TOMM70</h2>
+
+<h2>[94] TOR1B</h2>
+
+<h2>[95] WASHC4</h2>
+
+<h2>[96] WFS1[0-2346]</h2>
+
+<h2>[97] WFS1[2345-3216]</h2>
+
+<h2>[98] YIF1B</h2>
+
+<h2>411 Levels: AAR2 AASS … ZYG11B</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlcom{# This includes paralogs, recombinations found by DGINN and additionnal genes }
+\hlcom{# included on purpose}</p>
+
+<p>\hlcom{# Number of genes from the original list not present in DGINN output}
+\hlstd{tab[(tab}\hlopt{\(}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{\)}\hlstd{Gene)}\hlopt{==}\hlstd{F,}\hlstr{“Gene.name”}\hlstd{]}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] “ADCK4” “ARL6IP6”</h2>
+
+<h2>[3] “ATP5L” “C19orf52”</h2>
+
+<h2>[5] “C1orf50” “ERO1LB”</h2>
+
+<h2>[7] “FAM134C” “FGFR1OP”</h2>
+
+<h2>[9] “KIAA1033” “MFGE8”</h2>
+
+<h2>[11] “NUPL1” “SIGMAR1”</h2>
+
+<h2>[13] “SPG20” “TCEB1”</h2>
+
+<h2>[15] “TCEB2” “TOMM70A”</h2>
+
+<h2>[17] “USP13” “VIMP”</h2>
+
+<h2>[19] “WHSC1”</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“File”}\hlstd{,} \hlstr{“Name”}\hlstd{,} \hlstr{“Gene.name”}\hlstd{,} \hlstr{“GeneSize”}\hlstd{,}
+ \hlstr{“dginn-primate_NbSpecies”}\hlstd{,} \hlstr{“dginn-primate_omegaM0Bpp”}\hlstd{,}
+ \hlstr{“dginn-primate_omegaM0codeml”}\hlstd{,} \hlstr{“dginn-primate_BUSTED”}\hlstd{,}
+ \hlstr{“dginn-primate_BUSTED.p.value”}\hlstd{,} \hlstr{“dginn-primate_MEME.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_MEME.PSS”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2”}\hlstd{,}
+ \hlstr{“dginn-primate_BppM1M2.p.value”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_BppM1M2.PSS”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8”}\hlstd{,}
+ \hlstr{“dginn-primate_BppM7M8.p.value”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_BppM7M8.PSS”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2”}\hlstd{,}
+ \hlstr{“dginn-primate_codemlM1M2.p.value”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_codemlM1M2.PSS”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8”}\hlstd{,}
+ \hlstr{“dginn-primate_codemlM7M8.p.value”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_codemlM7M8.PSS”}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{\(}\hlstd{dginn-primate_BUSTED)}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{\)}\hlstd{<code>dginn-primate_codemlM1M2</code>)}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8)}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{\)}\hlstd{<code>dginn-primate_BppM1M2</code>)}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{$}\hlstd{<code>dginn-primate_BppM7M8</code>)}</p>
+
+<p>\hlkwd{table}\hlstd{(dginnT}\hlopt{\(}\hlstd{dginn-primate_BUSTED}\hlopt{==}\hlstr{“na”}\hlstd{,dginnT}\hlopt{\)}\hlstd{<code>dginn-primate_codemlM1M2</code>}\hlopt{==}\hlstr{“na”}\hlstd{, dginnT}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8}\hlopt{==}\hlstr{“na”}\hlstd{,}
+ \hlstd{dginnT}\hlopt{\)}\hlstd{<code>dginn-primate_BppM1M2</code>}\hlopt{==}\hlstr{“na”}\hlstd{, dginnT}\hlopt{$}\hlstd{<code>dginn-primate_BppM7M8</code>}\hlopt{==}\hlstr{“na”} \hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\subsection{Join Table and DGINN table}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnT,} \hlkwc{by}\hlstd{=}\hlstr{“Gene.name”}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}</p>
+
+<p>\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{<code>dginn-primate_BUSTED</code>)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>N na Y</h2>
+
+<h2>155 12 147</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{<code>dginn-primate_codemlM1M2</code>)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>N na Y</h2>
+
+<h2>216 26 72</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{<code>dginn-primate_codemlM7M8</code>)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>N na Y</h2>
+
+<h2>161 40 113</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{<code>dginn-primate_BppM1M2</code>)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>N na Y</h2>
+
+<h2>252 21 41</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{<code>dginn-primate_BppM7M8</code>)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>N na Y</h2>
+
+<h2>173 22 119</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{\(}\hlstd{dginn-primate_BUSTED}\hlopt{==}\hlstr{“na”} \hlopt{|} \hlstd{tab}\hlopt{\)}\hlstd{<code>dginn-primate_codemlM1M2</code>}\hlopt{==}\hlstr{“na”} \hlopt{|} \hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8}\hlopt{==}\hlstr{“na”} \hlopt{|}
+ \hlstd{tab}\hlopt{\)}\hlstd{<code>dginn-primate_BppM1M2</code>}\hlopt{==}\hlstr{“na”}\hlopt{|} \hlstd{tab}\hlopt{$}\hlstd{<code>dginn-primate_BppM7M8</code>}\hlopt{==}\hlstr{“na”} \hlstd{)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>FALSE TRUE</h2>
+
+<h2>274 40</h2>
+
+<p>\end{verbatim}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\subsection{Add DGINN results on bat dataset}</p>
+
+<p>DGINN results from different analysis.</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# original table}
+\hlstd{dginnbats}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{“data/DGINN_202005281339summary_cleaned.tab”}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}</p>
+
+<p>\hlcom{# rerun on corrected alignment}
+\hlstd{dginnbatsnew1}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{“data/DGINN_202011262248_summary.tab”}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
+\hlstd{dginnbatsnew2}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{“data/DGINN_202012192053_summary.tab”}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}</p>
+
+<p>\hlcom{# colomne choice, BUSTED and Bppml form first file, codeml from the other one}
+\hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew1}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{omegaM0codeml}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{omegaM0codeml}</p>
+
+<p>\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM1M2}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM1M2}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM1M2_p.value}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM1M2_p.value}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM1M2_NbSites}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM1M2_NbSites}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM1M2_PSS}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM1M2_PSS}</p>
+
+<p>\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM7M8}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM7M8}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM7M8_p.value}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM7M8_p.value}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM7M8_NbSites}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM7M8_NbSites}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM7M8_PSS}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM7M8_PSS}</p>
+
+<p>\hlcom{####}
+\hlcom{## RIPK1 is actually a primat results}
+\hlcom{## 1. Take it and put it at the right place}
+\hlstd{ripk1}\hlkwb{<-}\hlkwd{as.vector}\hlstd{(dginnbatsnew[dginnbatsnew}\hlopt{\(}\hlstd{Gene}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,])}
+\hlstd{tab}\hlopt{\)}\hlstd{<code>dginn-primate_omegaM0Bpp</code>}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{<code>dginn-primate_omegaM0Bpp</code>))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_BUSTED.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{<code>dginn-primate_BUSTED.p.value</code>))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_BppM1M2.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{<code>dginn-primate_BppM1M2.p.value</code>))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_BppM7M8.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{<code>dginn-primate_BppM7M8.p.value</code>))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_BppM7M8.PSS}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{<code>dginn-primate_BppM7M8.PSS</code>))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM1M2.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{<code>dginn-primate_codemlM1M2.p.value</code>))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM1M2.PSS}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{<code>dginn-primate_codemlM1M2.PSS</code>))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{<code>dginn-primate_codemlM7M8.p.value</code>))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8.PSS}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{<code>dginn-primate_codemlM7M8.PSS</code>))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“GeneSize”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{GeneSize}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_NbSpecies"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{NbSpecies}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_omegaM0Bpp"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{omegaM0Bpp}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_omegaM0codeml"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{omegaM0codeml}</p>
+
+<p>\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“dginn-primate_BUSTED”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BUSTED}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BUSTED.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BUSTED_p.value}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_MEME.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{MEME_NbSites}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_MEME.PSS"}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ripk1}\hlopt{\)}\hlstd{MEME_PSS))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“dginn-primate_BppM1M2”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM1M2}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM1M2_p.value}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM1M2_NbSites}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM1M2_PSS}</p>
+
+<p>\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“dginn-primate_BppM7M8”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM7M8}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM7M8_p.value}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM7M8_NbSites}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM7M8_PSS}</p>
+
+<p>\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“dginn-primate_codemlM1M2”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM1M2}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM1M2_p.value}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM1M2_NbSites}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM1M2_PSS}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM7M8}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM7M8_p.value}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM7M8_NbSites}
+\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM7M8_PSS}</p>
+
+<p>\hlcom{## 2. Remove it}
+\hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{!=}\hlstr{“RIPK1”}\hlstd{,]}</p>
+
+<p>\hlcom{## suppress redundant lines}
+\hlstd{dginnbats}\hlkwb{<-}\hlstd{dginnbats[(dginnbats}\hlopt{\(}\hlstd{Gene} \hlopt{%in%} \hlstd{dginnbatsnew}\hlopt{\)}\hlstd{Gene)}\hlopt{==}\hlnum{FALSE}\hlstd{,]}
+\hlkwd{names}\hlstd{(dginnbatsnew)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnbats)}</p>
+
+<p>\hlcom{##############“}
+\hlstd{dginnbatsnew[,}\hlnum{4}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(dginnbatsnew[,}\hlnum{4}\hlstd{])}
+\hlstd{dginnbats[,}\hlnum{6}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{6}\hlstd{]))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{dginnbats[,}\hlnum{8}\hlstd{]}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{8}\hlstd{])}
+\hlstd{dginnbats[,}\hlnum{12}\hlstd{]}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{12}\hlstd{])}
+\hlstd{dginnbats[,}\hlnum{13}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{13}\hlstd{]))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{dginnbats[,}\hlnum{16}\hlstd{]}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{16}\hlstd{])}
+\hlstd{dginnbats[,}\hlnum{17}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{17}\hlstd{]))}
+\end{alltt}</p>
+
+<p>{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlcom{## replace by new data}
+\hlstd{dginnbats}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnbats, dginnbatsnew)}</p>
+
+<p>\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File”}\hlstd{,} \hlstr{“bats<em>Name”}\hlstd{,} \hlstr{“cooper.batsGene”}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{“bats</em>”}\hlstd{,}
+ \hlkwd{names}\hlstd{(dginnbats)[}\hlopt{-}\hlstd{(}\hlnum{1}\hlopt{:}\hlnum{3}\hlstd{)]))}
+\hlkwd{names}\hlstd{(dginnbats)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] “File”</h2>
+
+<h2>[2] “bats_Name”</h2>
+
+<h2>[3] “cooper.batsGene”</h2>
+
+<h2>[4] “bats_GeneSize”</h2>
+
+<h2>[5] “bats_NbSpecies”</h2>
+
+<h2>[6] “bats_omegaM0Bpp”</h2>
+
+<h2>[7] “bats_omegaM0codeml”</h2>
+
+<h2>[8] “bats_BUSTED”</h2>
+
+<h2>[9] “bats_BUSTED.p.value”</h2>
+
+<h2>[10] “bats_MEME.NbSites”</h2>
+
+<h2>[11] “bats_MEME.PSS”</h2>
+
+<h2>[12] “bats_BppM1M2”</h2>
+
+<h2>[13] “bats_BppM1M2.p.value”</h2>
+
+<h2>[14] “bats_BppM1M2.NbSites”</h2>
+
+<h2>[15] “bats_BppM1M2.PSS”</h2>
+
+<h2>[16] “bats_BppM7M8”</h2>
+
+<h2>[17] “bats_BppM7M8.p.value”</h2>
+
+<h2>[18] “bats_BppM7M8.NbSites”</h2>
+
+<h2>[19] “bats_BppM7M8.PSS”</h2>
+
+<h2>[20] “bats_codemlM1M2”</h2>
+
+<h2>[21] “bats_codemlM1M2.p.value”</h2>
+
+<h2>[22] “bats_codemlM1M2.NbSites”</h2>
+
+<h2>[23] “bats_codemlM1M2.PSS”</h2>
+
+<h2>[24] “bats_codemlM7M8”</h2>
+
+<h2>[25] “bats_codemlM7M8.p.value”</h2>
+
+<h2>[26] “bats_codemlM7M8.NbSites”</h2>
+
+<h2>[27] “bats_codemlM7M8.PSS”</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnbats,} \hlkwc{by}\hlstd{=}\hlstr{“cooper.batsGene”}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\subsection{Write the new table}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{write.table}\hlstd{(tab,} \hlstr{“covid_comp_complete.txt”}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{“\textbackslash{}t”}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\section{Second Table}</p>
+
+<p>Table containing the DGINN results for both Primates and bats. Conserve all genes.</p>
+
+<p>\subsection{Primates}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnT}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{“data/DGINN_202005281649summary_cleaned.csv”}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{“,”}\hlstd{)}</p>
+
+<p>\hlkwd{dim}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 412 27</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{names}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] “File”</h2>
+
+<h2>[2] “Name”</h2>
+
+<h2>[3] “Gene”</h2>
+
+<h2>[4] “GeneSize”</h2>
+
+<h2>[5] “NbSpecies”</h2>
+
+<h2>[6] “omegaM0Bpp”</h2>
+
+<h2>[7] “omegaM0codeml”</h2>
+
+<h2>[8] “BUSTED”</h2>
+
+<h2>[9] “BUSTED.p.value”</h2>
+
+<h2>[10] “MEME.NbSites”</h2>
+
+<h2>[11] “MEME.PSS”</h2>
+
+<h2>[12] “BppM1M2”</h2>
+
+<h2>[13] “BppM1M2.p.value”</h2>
+
+<h2>[14] “BppM1M2.NbSites”</h2>
+
+<h2>[15] “BppM1M2.PSS”</h2>
+
+<h2>[16] “BppM7M8”</h2>
+
+<h2>[17] “BppM7M8.p.value”</h2>
+
+<h2>[18] “BppM7M8.NbSites”</h2>
+
+<h2>[19] “BppM7M8.PSS”</h2>
+
+<h2>[20] “codemlM1M2”</h2>
+
+<h2>[21] “codemlM1M2.p.value”</h2>
+
+<h2>[22] “codemlM1M2.NbSites”</h2>
+
+<h2>[23] “codemlM1M2.PSS”</h2>
+
+<h2>[24] “codemlM7M8”</h2>
+
+<h2>[25] “codemlM7M8.p.value”</h2>
+
+<h2>[26] “codemlM7M8.NbSites”</h2>
+
+<h2>[27] “codemlM7M8.PSS”</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlcom{# Rename the columns to include primate}
+\hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“File”}\hlstd{,} \hlstr{“Name”}\hlstd{,} \hlstr{“Gene.name”}\hlstd{,} \hlstr{“GeneSize”}\hlstd{,}
+ \hlstr{“dginn-primate_NbSpecies”}\hlstd{,} \hlstr{“dginn-primate_omegaM0Bpp”}\hlstd{,}
+ \hlstr{“dginn-primate_omegaM0codeml”}\hlstd{,} \hlstr{“dginn-primate_BUSTED”}\hlstd{,}
+ \hlstr{“dginn-primate_BUSTED.p.value”}\hlstd{,} \hlstr{“dginn-primate_MEME.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_MEME.PSS”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2”}\hlstd{,}
+ \hlstr{“dginn-primate_BppM1M2.p.value”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_BppM1M2.PSS”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8”}\hlstd{,}
+ \hlstr{“dginn-primate_BppM7M8.p.value”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_BppM7M8.PSS”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2”}\hlstd{,}
+ \hlstr{“dginn-primate_codemlM1M2.p.value”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_codemlM1M2.PSS”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8”}\hlstd{,}
+ \hlstr{“dginn-primate_codemlM7M8.p.value”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8.NbSites”}\hlstd{,}
+ \hlstr{“dginn-primate_codemlM7M8.PSS”}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\subsection{Bats}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# original table}
+\hlstd{dginnbats}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{“data/DGINN_202005281339summary_cleaned-LE201108.txt”}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}</p>
+
+<p>\hlcom{# rerun on corrected alignment}
+\hlstd{dginnbatsnew}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{“data/DGINN_202011262248_hyphybpp-202012192053_codeml-summary.txt”}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Add both columns }
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{Lucie.s.comments}\hlkwb{<-}\hlstr{""}
+\hlstd{dginnbatsnew}\hlopt{\)}\hlstd{Action.taken}\hlkwb{<-}\hlstr{""}</p>
+
+<p>\hlcom{# Homogenize column names}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{BUSTED_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BUSTED.p.value}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{MEME_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{MEME.NbSites}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{MEME_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{MEME.PSS}</p>
+
+<p>\hlstd{dginnbats}\hlopt{\(}\hlstd{BppM1M2_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM1M2.p.value}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{BppM1M2_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM1M2.NbSites}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{BppM1M2_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM1M2.PSS}</p>
+
+<p>\hlstd{dginnbats}\hlopt{\(}\hlstd{BppM7M8_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM7M8.p.value}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{BppM7M8_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM7M8.NbSites}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{BppM7M8_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM7M8.PSS}</p>
+
+<p>\hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM1M2_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM1M2.p.value}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM1M2_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM1M2.NbSites}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM1M2_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM1M2.PSS}</p>
+
+<p>\hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM7M8_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM7M8.p.value}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM7M8_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM7M8.NbSites}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM7M8_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM7M8.PSS}
+\end{alltt}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Order columns in the same order in both tables}
+\hlstd{dginnbats}\hlkwb{<-}\hlstd{dginnbats[,}\hlkwd{names}\hlstd{(dginnbatsnew)]}</p>
+
+<p>\hlkwd{names}\hlstd{(dginnbatsnew)} \hlopt{%in%} \hlkwd{names}\hlstd{(dginnbats)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[6] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[11] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[16] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[21] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[26] TRUE TRUE TRUE TRUE</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{names}\hlstd{(dginnbats)}\hlopt{==}\hlkwd{names}\hlstd{(dginnbatsnew)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[6] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[11] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[16] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[21] TRUE TRUE TRUE TRUE TRUE</h2>
+
+<h2>[26] TRUE TRUE TRUE TRUE</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlcom{# Put RIPK aside}
+\hlstd{ripk1}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlnum{1}\hlopt{:}\hlnum{27}\hlstd{]}</p>
+
+<p>\hlcom{# Add it to primate table}
+\hlkwd{names}\hlstd{(ripk1)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnT)}</p>
+
+<p>\hlstd{ripk1}\hlopt{\(}\hlstd{dginn-primate_omegaM0Bpp}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{\)}\hlstd{<code>dginn-primate_omegaM0Bpp</code>)}
+\hlstd{ripk1}\hlopt{\(}\hlstd{dginn-primate_BUSTED.p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{\)}\hlstd{<code>dginn-primate_BUSTED.p.value</code>)}
+\hlstd{ripk1}\hlopt{\(}\hlstd{dginn-primate_BppM1M2.p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{\)}\hlstd{<code>dginn-primate_BppM1M2.p.value</code>)}
+\hlstd{ripk1}\hlopt{\(}\hlstd{dginn-primate_BppM7M8.p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{\)}\hlstd{<code>dginn-primate_BppM7M8.p.value</code>)}</p>
+
+<p>\hlstd{dginnT}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnT, ripk1)}</p>
+
+<p>\hlcom{## Remove it Ripk1 from bats}
+\hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{!=}\hlstr{“RIPK1”}\hlstd{,]}</p>
+
+<p>\hlcom{## suppress redundant lines}
+\hlstd{dginnbats}\hlkwb{<-}\hlstd{dginnbats[(dginnbats}\hlopt{\(}\hlstd{Gene} \hlopt{%in%} \hlstd{dginnbatsnew}\hlopt{\)}\hlstd{Gene)}\hlopt{==}\hlnum{FALSE}\hlstd{,]}
+\hlkwd{names}\hlstd{(dginnbatsnew)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnbats)}</p>
+
+<p>\hlcom{## replace by new data}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{omegaM0Bpp}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(dginnbatsnew}\hlopt{\)}\hlstd{omegaM0Bpp)}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{BppM1M2_p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(dginnbatsnew}\hlopt{\)}\hlstd{BppM1M2_p.value)}
+\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{BppM7M8_p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(dginnbatsnew}\hlopt{\)}\hlstd{BppM7M8_p.value)}</p>
+
+<p>\hlstd{dginnbats}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnbats, dginnbatsnew)}</p>
+
+<p>\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“bats<em>File”}\hlstd{,} \hlstr{“bats_Name”}\hlstd{,} \hlstr{“Gene.name”}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{“bats</em>”}\hlstd{,}
+ \hlkwd{names}\hlstd{(dginnbats)[}\hlopt{-}\hlstd{(}\hlnum{1}\hlopt{:}\hlnum{3}\hlstd{)]))}
+\hlkwd{names}\hlstd{(dginnbats)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] “bats_File”</h2>
+
+<h2>[2] “bats_Name”</h2>
+
+<h2>[3] “Gene.name”</h2>
+
+<h2>[4] “bats_GeneSize”</h2>
+
+<h2>[5] “bats_NbSpecies”</h2>
+
+<h2>[6] “bats_omegaM0Bpp”</h2>
+
+<h2>[7] “bats_omegaM0codeml”</h2>
+
+<h2>[8] “bats_BUSTED”</h2>
+
+<h2>[9] “bats_BUSTED_p.value”</h2>
+
+<h2>[10] “bats_MEME_NbSites”</h2>
+
+<h2>[11] “bats_MEME_PSS”</h2>
+
+<h2>[12] “bats_BppM1M2”</h2>
+
+<h2>[13] “bats_BppM1M2_p.value”</h2>
+
+<h2>[14] “bats_BppM1M2_NbSites”</h2>
+
+<h2>[15] “bats_BppM1M2_PSS”</h2>
+
+<h2>[16] “bats_BppM7M8”</h2>
+
+<h2>[17] “bats_BppM7M8_p.value”</h2>
+
+<h2>[18] “bats_BppM7M8_NbSites”</h2>
+
+<h2>[19] “bats_BppM7M8_PSS”</h2>
+
+<h2>[20] “bats_codemlM1M2”</h2>
+
+<h2>[21] “bats_codemlM1M2_p.value”</h2>
+
+<h2>[22] “bats_codemlM1M2_NbSites”</h2>
+
+<h2>[23] “bats_codemlM1M2_PSS”</h2>
+
+<h2>[24] “bats_codemlM7M8”</h2>
+
+<h2>[25] “bats_codemlM7M8_p.value”</h2>
+
+<h2>[26] “bats_codemlM7M8_NbSites”</h2>
+
+<h2>[27] “bats_codemlM7M8_PSS”</h2>
+
+<h2>[28] “bats_Lucie.s.comments”</h2>
+
+<h2>[29] “bats_Action.taken”</h2>
+
+<p>\end{verbatim}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\subsection{Merged table}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tidy.opts} \hlkwb{=} \hlkwd{list}\hlstd{(}\hlkwc{width.cutoff} \hlstd{=} \hlnum{30}\hlstd{)}
+\hlkwd{dim}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 413 27</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] AAR2</h2>
+
+<h2>[2] AASS</h2>
+
+<h2>[3] AATF</h2>
+
+<h2>[4] ABCC1</h2>
+
+<h2>[5] ACAD9</h2>
+
+<h2>[6] ACADM</h2>
+
+<h2>[7] ACE2</h2>
+
+<h2>[8] ACSL3</h2>
+
+<h2>[9] ADAM9</h2>
+
+<h2>[10] ADAM9[0-3120]</h2>
+
+<h2>[11] ADAM9[3119-3927]</h2>
+
+<h2>[12] ADAMTS1</h2>
+
+<h2>[13] AGPS</h2>
+
+<h2>[14] AKAP8</h2>
+
+<h2>[15] AKAP8L</h2>
+
+<h2>[16] AKAP9</h2>
+
+<h2>[17] ALG11</h2>
+
+<h2>[18] ALG5</h2>
+
+<h2>[19] ALG8</h2>
+
+<h2>[20] ANO6</h2>
+
+<h2>[21] AP2A2</h2>
+
+<h2>[22] AP2M1</h2>
+
+<h2>[23] AP3B1</h2>
+
+<h2>[24] ARF6</h2>
+
+<h2>[25] ATE1</h2>
+
+<h2>[26] ATP13A3</h2>
+
+<h2>[27] ATP1B1</h2>
+
+<h2>[28] ATP5MGL</h2>
+
+<h2>[29] ATP6AP1</h2>
+
+<h2>[30] ATP6V1A</h2>
+
+<h2>[31] BAG5</h2>
+
+<h2>[32] BCKDK</h2>
+
+<h2>[33] BCS1L</h2>
+
+<h2>[34] BRD2</h2>
+
+<h2>[35] BRD4</h2>
+
+<h2>[36] BZW2</h2>
+
+<h2>[37] C1H1ORF50</h2>
+
+<h2>[38] CCDC86</h2>
+
+<h2>[39] CDK5RAP2</h2>
+
+<h2>[40] CENPF</h2>
+
+<h2>[41] CEP112</h2>
+
+<h2>[42] CEP135</h2>
+
+<h2>[43] CEP135[0-3264]</h2>
+
+<h2>[44] CEP135[3263-3678]</h2>
+
+<h2>[45] CEP250</h2>
+
+<h2>[46] CEP350</h2>
+
+<h2>[47] CEP43</h2>
+
+<h2>[48] CEP68</h2>
+
+<h2>[49] CHMP2A</h2>
+
+<h2>[50] CHPF</h2>
+
+<h2>[51] CHPF2</h2>
+
+<h2>[52] CISD3</h2>
+
+<h2>[53] CIT</h2>
+
+<h2>[54] CLCC1</h2>
+
+<h2>[55] CLIP4</h2>
+
+<h2>[56] CNTRL</h2>
+
+<h2>[57] COL6A1</h2>
+
+<h2>[58] COLGALT1</h2>
+
+<h2>[59] COMT</h2>
+
+<h2>[60] COQ8B</h2>
+
+<h2>[61] COQ8A</h2>
+
+<h2>[62] CRTC3</h2>
+
+<h2>[63] CSDE1</h2>
+
+<h2>[64] CSNK2A1</h2>
+
+<h2>[65] CSNK2A2</h2>
+
+<h2>[66] CSNK2B</h2>
+
+<h2>[67] CSNK2B[0-609]</h2>
+
+<h2>[68] CSNK2B[608-2568]</h2>
+
+<h2>[69] CUL2</h2>
+
+<h2>[70] CWC27</h2>
+
+<h2>[71] CYB5B</h2>
+
+<h2>[72] CYB5R3</h2>
+
+<h2>[73] CYB5R1</h2>
+
+<h2>[74] DCAF7</h2>
+
+<h2>[75] DCAKD</h2>
+
+<h2>[76] DCTPP1</h2>
+
+<h2>[77] DDX10</h2>
+
+<h2>[78] DDX21</h2>
+
+<h2>[79] DDX21[0-717]</h2>
+
+<h2>[80] DDX21[716-2538]</h2>
+
+<h2>[81] DDX50</h2>
+
+<h2>[82] DNAJC11</h2>
+
+<h2>[83] DNAJC19</h2>
+
+<h2>[84] DNAJC15</h2>
+
+<h2>[85] DNMT1</h2>
+
+<h2>[86] DPH5</h2>
+
+<h2>[87] DPH5[0-702]</h2>
+
+<h2>[88] DPH5[701-1326]</h2>
+
+<h2>[89] DPY19L2</h2>
+
+<h2>[90] DPY19L1</h2>
+
+<h2>[91] ECSIT</h2>
+
+<h2>[92] EDEM3</h2>
+
+<h2>[93] EIF4E2</h2>
+
+<h2>[94] EIF4H</h2>
+
+<h2>[95] ELOC</h2>
+
+<h2>[96] EMC1</h2>
+
+<h2>[97] ERC1</h2>
+
+<h2>[98] ERGIC1</h2>
+
+<h2>[99] ERLEC1</h2>
+
+<h2>[100] ERMP1</h2>
+
+<h2>[101] ERO1B</h2>
+
+<h2>[102] ERP44</h2>
+
+<h2>[103] ETFA</h2>
+
+<h2>[104] EXOSC2</h2>
+
+<h2>[105] EXOSC3</h2>
+
+<h2>[106] EXOSC3[0-1446]</h2>
+
+<h2>[107] EXOSC3[1445-1980]</h2>
+
+<h2>[108] EXOSC5</h2>
+
+<h2>[109] EXOSC8</h2>
+
+<h2>[110] F2RL1</h2>
+
+<h2>[111] FAM162A</h2>
+
+<h2>[112] FAM8A1</h2>
+
+<h2>[113] FAM98A</h2>
+
+<h2>[114] FAR2</h2>
+
+<h2>[115] FASTKD5</h2>
+
+<h2>[116] FBLN5</h2>
+
+<h2>[117] FBN1</h2>
+
+<h2>[118] FBN3</h2>
+
+<h2>[119] FBN2</h2>
+
+<h2>[120] FBXL12</h2>
+
+<h2>[121] FKBP10</h2>
+
+<h2>[122] FKBP15</h2>
+
+<h2>[123] FKBP7</h2>
+
+<h2>[124] FOXRED2</h2>
+
+<h2>[125] FYCO1</h2>
+
+<h2>[126] G3BP1</h2>
+
+<h2>[127] G3BP2</h2>
+
+<h2>[128] GCC1</h2>
+
+<h2>[129] GCC2</h2>
+
+<h2>[130] GDF15</h2>
+
+<h2>[131] GFER</h2>
+
+<h2>[132] GGCX</h2>
+
+<h2>[133] GGH</h2>
+
+<h2>[134] GHITM</h2>
+
+<h2>[135] GIGYF2</h2>
+
+<h2>[136] GLA</h2>
+
+<h2>[137] GNB4</h2>
+
+<h2>[138] GNB2</h2>
+
+<h2>[139] GNB1</h2>
+
+<h2>[140] GNB3</h2>
+
+<h2>[141] GNG5</h2>
+
+<h2>[142] GNG5</h2>
+
+<h2>[143] GOLGA2</h2>
+
+<h2>[144] GOLGA3</h2>
+
+<h2>[145] GOLGA7</h2>
+
+<h2>[146] GOLGA7[0-312]</h2>
+
+<h2>[147] GOLGA7[311-549]</h2>
+
+<h2>[148] GOLGB1</h2>
+
+<h2>[149] GORASP1</h2>
+
+<h2>[150] GPAA1</h2>
+
+<h2>[151] GPX1</h2>
+
+<h2>[152] GPX1[0-1218]</h2>
+
+<h2>[153] GPX1[1217-2946]</h2>
+
+<h2>[154] GRIPAP1</h2>
+
+<h2>[155] GRPEL1</h2>
+
+<h2>[156] GTF2F2</h2>
+
+<h2>[157] HDAC2</h2>
+
+<h2>[158] HDAC1</h2>
+
+<h2>[159] HEATR3</h2>
+
+<h2>[160] HECTD1</h2>
+
+<h2>[161] HMOX1</h2>
+
+<h2>[162] HOOK1</h2>
+
+<h2>[163] HS2ST1</h2>
+
+<h2>[164] HS6ST2</h2>
+
+<h2>[165] HS6ST3</h2>
+
+<h2>[166] HSBP1</h2>
+
+<h2>[167] HYOU1</h2>
+
+<h2>[168] IDE</h2>
+
+<h2>[169] IL17RA</h2>
+
+<h2>[170] IMPDH1</h2>
+
+<h2>[171] IMPDH2</h2>
+
+<h2>[172] INHBE</h2>
+
+<h2>[173] INTS4</h2>
+
+<h2>[174] ITGB1</h2>
+
+<h2>[175] ITGB1[0-2328]</h2>
+
+<h2>[176] ITGB1[2327-2844]</h2>
+
+<h2>[177] JAKMIP1</h2>
+
+<h2>[178] LARP1</h2>
+
+<h2>[179] LARP4B</h2>
+
+<h2>[180] LARP7</h2>
+
+<h2>[181] LMAN2</h2>
+
+<h2>[182] LMAN2L</h2>
+
+<h2>[183] LOX</h2>
+
+<h2>[184] MAP7D1</h2>
+
+<h2>[185] MARK1</h2>
+
+<h2>[186] MARK2</h2>
+
+<h2>[187] MARK3</h2>
+
+<h2>[188] MAT2B</h2>
+
+<h2>[189] MDN1</h2>
+
+<h2>[190] MEPCE</h2>
+
+<h2>[191] MIB1</h2>
+
+<h2>[192] MIPOL1</h2>
+
+<h2>[193] MOGS</h2>
+
+<h2>[194] MOV10</h2>
+
+<h2>[195] MPHOSPH10</h2>
+
+<h2>[196] MRPS2</h2>
+
+<h2>[197] MRPS25</h2>
+
+<h2>[198] MRPS27</h2>
+
+<h2>[199] MRPS5</h2>
+
+<h2>[200] MRPS5[0-1569]</h2>
+
+<h2>[201] MRPS5[1568-3783]</h2>
+
+<h2>[202] MARC1</h2>
+
+<h2>[203] MARC2</h2>
+
+<h2>[204] MTCH1</h2>
+
+<h2>[205] MYCBP2</h2>
+
+<h2>[206] MGRN1</h2>
+
+<h2>[207] NARS2</h2>
+
+<h2>[208] NAT14</h2>
+
+<h2>[209] NDFIP2</h2>
+
+<h2>[210] NDFIP2[0-768]</h2>
+
+<h2>[211] NDFIP2[767-1314]</h2>
+
+<h2>[212] NDUFAF1</h2>
+
+<h2>[213] NDUFAF2</h2>
+
+<h2>[214] NDUFAF2[0-258]</h2>
+
+<h2>[215] NDUFAF2[257-744]</h2>
+
+<h2>[216] NDUFB9</h2>
+
+<h2>[217] NEK9</h2>
+
+<h2>[218] NEU1</h2>
+
+<h2>[219] NGDN</h2>
+
+<h2>[220] NGLY1</h2>
+
+<h2>[221] NIN</h2>
+
+<h2>[222] NINL</h2>
+
+<h2>[223] NLRX1</h2>
+
+<h2>[224] NOL10</h2>
+
+<h2>[225] NPC2</h2>
+
+<h2>[226] NPTX1</h2>
+
+<h2>[227] NSD2</h2>
+
+<h2>[228] NUP210</h2>
+
+<h2>[229] NUP214</h2>
+
+<h2>[230] NUP54</h2>
+
+<h2>[231] NUP58</h2>
+
+<h2>[232] NUP58[0-1824]</h2>
+
+<h2>[233] NUP58[1823-2367]</h2>
+
+<h2>[234] NUP62</h2>
+
+<h2>[235] NUP88</h2>
+
+<h2>[236] NUP98</h2>
+
+<h2>[237] NUTF2</h2>
+
+<h2>[238] OS9</h2>
+
+<h2>[239] PABPC3</h2>
+
+<h2>[240] POTPABPC1</h2>
+
+<h2>[241] PABPC1</h2>
+
+<h2>[242] PABPC4</h2>
+
+<h2>[243] PABPC4L</h2>
+
+<h2>[244] PABPC5</h2>
+
+<h2>[245] PCNT</h2>
+
+<h2>[246] PCSK6</h2>
+
+<h2>[247] PCSK5</h2>
+
+<h2>[248] PDE4DIP</h2>
+
+<h2>[249] PDZD11</h2>
+
+<h2>[250] PIGO</h2>
+
+<h2>[251] PIGS</h2>
+
+<h2>[252] PITRM1</h2>
+
+<h2>[253] PKP2</h2>
+
+<h2>[254] PLAT</h2>
+
+<h2>[255] PLD3</h2>
+
+<h2>[256] PLEKHA5</h2>
+
+<h2>[257] PLEKHF2</h2>
+
+<h2>[258] PLOD2</h2>
+
+<h2>[259] PMPCA</h2>
+
+<h2>[260] PMPCB</h2>
+
+<h2>[261] POFUT1</h2>
+
+<h2>[262] KDELC1</h2>
+
+<h2>[263] KDELC2</h2>
+
+<h2>[264] POLA1</h2>
+
+<h2>[265] POLA2</h2>
+
+<h2>[266] POR</h2>
+
+<h2>[267] PPIL3</h2>
+
+<h2>[268] PPT1</h2>
+
+<h2>[269] PRIM1</h2>
+
+<h2>[270] PRIM2</h2>
+
+<h2>[271] PRIM2[0-1071]</h2>
+
+<h2>[272] PRIM2[1070-1902]</h2>
+
+<h2>[273] PRKACB</h2>
+
+<h2>[274] PRKACG</h2>
+
+<h2>[275] PRKACA</h2>
+
+<h2>[276] PRKAR2A</h2>
+
+<h2>[277] PRKAR2B</h2>
+
+<h2>[278] PRRC2B</h2>
+
+<h2>[279] PSMD8</h2>
+
+<h2>[280] PTBP2</h2>
+
+<h2>[281] PTGES2</h2>
+
+<h2>[282] PTGES2[0-1587]</h2>
+
+<h2>[283] PTGES2[1586-2202]</h2>
+
+<h2>[284] PUSL1</h2>
+
+<h2>[285] PVR</h2>
+
+<h2>[286] QSOX2</h2>
+
+<h2>[287] RAB10</h2>
+
+<h2>[288] RAB8B</h2>
+
+<h2>[289] RAB13</h2>
+
+<h2>[290] RAB14</h2>
+
+<h2>[291] RAB18</h2>
+
+<h2>[292] RAB18[0-855]</h2>
+
+<h2>[293] RAB18[854-1815]</h2>
+
+<h2>[294] RAB1A</h2>
+
+<h2>[295] RAB2B</h2>
+
+<h2>[296] RAB2A</h2>
+
+<h2>[297] RAB5C</h2>
+
+<h2>[298] RAB5A</h2>
+
+<h2>[299] RAB5B</h2>
+
+<h2>[300] RAB7A</h2>
+
+<h2>[301] RAB15</h2>
+
+<h2>[302] RAB8A</h2>
+
+<h2>[303] RAE1</h2>
+
+<h2>[304] RALB</h2>
+
+<h2>[305] RALA</h2>
+
+<h2>[306] RAP1GDS1</h2>
+
+<h2>[307] RBM28</h2>
+
+<h2>[308] RBM41</h2>
+
+<h2>[309] RBX1</h2>
+
+<h2>[310] EZR</h2>
+
+<h2>[311] EZR[0-1458]</h2>
+
+<h2>[312] EZR[1457-3771]</h2>
+
+<h2>[313] RDX</h2>
+
+<h2>[314] MSN</h2>
+
+<h2>[315] REEP5</h2>
+
+<h2>[316] REEP6</h2>
+
+<h2>[317] RETREG3</h2>
+
+<h2>[318] RHOB</h2>
+
+<h2>[319] RHOC</h2>
+
+<h2>[320] RHOA</h2>
+
+<h2>[321] RIPK1</h2>
+
+<h2>[322] RNF41</h2>
+
+<h2>[323] RPL36</h2>
+
+<h2>[324] RRP9</h2>
+
+<h2>[325] RTN4</h2>
+
+<h2>[326] SAAL1</h2>
+
+<h2>[327] SBNO1</h2>
+
+<h2>[328] SCAP</h2>
+
+<h2>[329] SCARB1</h2>
+
+<h2>[330] SCCPDH</h2>
+
+<h2>[331] SDF2</h2>
+
+<h2>[332] SEPSECS</h2>
+
+<h2>[333] SIL1</h2>
+
+<h2>[334] SIRT5</h2>
+
+<h2>[335] SLC25A21</h2>
+
+<h2>[336] SLC27A2</h2>
+
+<h2>[337] SLC30A6</h2>
+
+<h2>[338] SLC30A7</h2>
+
+<h2>[339] SLC30A9</h2>
+
+<h2>[340] SLC44A2</h2>
+
+<h2>[341] SLC44A2[0-2577]</h2>
+
+<h2>[342] SLC44A2[2576-3657]</h2>
+
+<h2>[343] SLC9A3R1</h2>
+
+<h2>[344] SLU7</h2>
+
+<h2>[345] SMOC1</h2>
+
+<h2>[346] SNIP1</h2>
+
+<h2>[347] SPART</h2>
+
+<h2>[348] SRP19</h2>
+
+<h2>[349] SRP54</h2>
+
+<h2>[350] SRP72</h2>
+
+<h2>[351] SRP72[0-2604]</h2>
+
+<h2>[352] SRP72[2603-3417]</h2>
+
+<h2>[353] STC2</h2>
+
+<h2>[354] STOM</h2>
+
+<h2>[355] STOM[0-1047]</h2>
+
+<h2>[356] STOM[1046-1800]</h2>
+
+<h2>[357] STOML3</h2>
+
+<h2>[358] STOML2</h2>
+
+<h2>[359] SUN2</h2>
+
+<h2>[360] TAPT1</h2>
+
+<h2>[361] TARS2</h2>
+
+<h2>[362] TBCA</h2>
+
+<h2>[363] TBK1</h2>
+
+<h2>[364] TBKBP1</h2>
+
+<h2>[365] TCF12</h2>
+
+<h2>[366] THTPA</h2>
+
+<h2>[367] TIMM10</h2>
+
+<h2>[368] TIMM10B</h2>
+
+<h2>[369] TIMM29</h2>
+
+<h2>[370] TIMM8B</h2>
+
+<h2>[371] TIMM9</h2>
+
+<h2>[372] TLE1</h2>
+
+<h2>[373] TLE3</h2>
+
+<h2>[374] TLE4</h2>
+
+<h2>[375] TLE2</h2>
+
+<h2>[376] TLE2[0-1302]</h2>
+
+<h2>[377] TLE2[1301-3987]</h2>
+
+<h2>[378] AES</h2>
+
+<h2>[379] TM2D3</h2>
+
+<h2>[380] TMED5</h2>
+
+<h2>[381] TMEM39B</h2>
+
+<h2>[382] TMEM97</h2>
+
+<h2>[383] TMPRSS2</h2>
+
+<h2>[384] TOMM70</h2>
+
+<h2>[385] TOR1A</h2>
+
+<h2>[386] TOR1B</h2>
+
+<h2>[387] TOR1AIP1</h2>
+
+<h2>[388] TRIM59</h2>
+
+<h2>[389] TRMT1</h2>
+
+<h2>[390] TUBGCP2</h2>
+
+<h2>[391] TUBGCP3</h2>
+
+<h2>[392] TYSND1</h2>
+
+<h2>[393] UBAP2</h2>
+
+<h2>[394] UBAP2L</h2>
+
+<h2>[395] UBXN8</h2>
+
+<h2>[396] UGGT2</h2>
+
+<h2>[397] UPF1</h2>
+
+<h2>[398] USP54</h2>
+
+<h2>[399] VPS11</h2>
+
+<h2>[400] VPS39</h2>
+
+<h2>[401] WASHC4</h2>
+
+<h2>[402] WFS1</h2>
+
+<h2>[403] WFS1[0-2346]</h2>
+
+<h2>[404] WFS1[2345-3216]</h2>
+
+<h2>[405] YIF1A</h2>
+
+<h2>[406] YIF1B</h2>
+
+<h2>[407] ZC3H18</h2>
+
+<h2>[408] ZC3H7A</h2>
+
+<h2>[409] ZDHHC5</h2>
+
+<h2>[410] ZNF318</h2>
+
+<h2>[411] ZNF503</h2>
+
+<h2>[412] ZYG11B</h2>
+
+<h2>[413] RIPK1</h2>
+
+<h2>416 Levels: AAR2 AASS … SELENOS</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{dim}\hlstd{(dginnbats)}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 353 29</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] AAR2</h2>
+
+<h2>[2] AASS</h2>
+
+<h2>[3] AATF</h2>
+
+<h2>[4] ABCC1</h2>
+
+<h2>[5] ACAD9</h2>
+
+<h2>[6] ACADM</h2>
+
+<h2>[7] ACE2</h2>
+
+<h2>[8] ACSL3</h2>
+
+<h2>[9] ADAM9</h2>
+
+<h2>[10] ADAM9[0-2769]</h2>
+
+<h2>[11] ADAM9[2768-3030]</h2>
+
+<h2>[12] ADAMTS1</h2>
+
+<h2>[13] AGPS</h2>
+
+<h2>[14] AKAP8</h2>
+
+<h2>[15] AKAP8L</h2>
+
+<h2>[16] AKAP9</h2>
+
+<h2>[17] ALG11</h2>
+
+<h2>[18] ALG5</h2>
+
+<h2>[19] ALG8</h2>
+
+<h2>[20] ANO6</h2>
+
+<h2>[21] AP2A2</h2>
+
+<h2>[22] AP2M1</h2>
+
+<h2>[23] AP3B1</h2>
+
+<h2>[24] ARF6</h2>
+
+<h2>[25] ARL6IP6</h2>
+
+<h2>[26] ATP13A3</h2>
+
+<h2>[27] ATP1B1</h2>
+
+<h2>[28] ATP5MG</h2>
+
+<h2>[29] ATP6AP1</h2>
+
+<h2>[30] ATP6V1A</h2>
+
+<h2>[31] BAG5</h2>
+
+<h2>[32] BCKDK</h2>
+
+<h2>[33] BCS1</h2>
+
+<h2>[34] BRD2</h2>
+
+<h2>[35] BRD4</h2>
+
+<h2>[36] BZW2</h2>
+
+<h2>[37] CUNH1ORF50</h2>
+
+<h2>[38] CCDC86</h2>
+
+<h2>[39] CDK5RAP2</h2>
+
+<h2>[40] CENPF</h2>
+
+<h2>[41] CEP112</h2>
+
+<h2>[42] CEP135</h2>
+
+<h2>[43] CEP250</h2>
+
+<h2>[44] CEP350</h2>
+
+<h2>[45] CEP68</h2>
+
+<h2>[46] CHMP2A</h2>
+
+<h2>[47] CHPF</h2>
+
+<h2>[48] CHPF2</h2>
+
+<h2>[49] CISD3</h2>
+
+<h2>[50] CIT</h2>
+
+<h2>[51] CLCC1</h2>
+
+<h2>[52] CLIP4</h2>
+
+<h2>[53] CNTRL</h2>
+
+<h2>[54] COLGALT1</h2>
+
+<h2>[55] COMT</h2>
+
+<h2>[56] CRTC3</h2>
+
+<h2>[57] CSDE1</h2>
+
+<h2>[58] CSNK2A2</h2>
+
+<h2>[59] CSNK2B</h2>
+
+<h2>[60] CUL2</h2>
+
+<h2>[61] CWC27</h2>
+
+<h2>[62] CYB5BR3</h2>
+
+<h2>[63] DCAF7</h2>
+
+<h2>[64] DCAKD</h2>
+
+<h2>[65] DCTPP1</h2>
+
+<h2>[66] DDX10</h2>
+
+<h2>[67] DNAJC11</h2>
+
+<h2>[68] DNAJC19</h2>
+
+<h2>[69] DNMT1</h2>
+
+<h2>[70] DPH5</h2>
+
+<h2>[71] DPY19L1</h2>
+
+<h2>[72] ECSIT</h2>
+
+<h2>[73] EDEM3</h2>
+
+<h2>[74] EIF4E2</h2>
+
+<h2>[75] EIF4H</h2>
+
+<h2>[76] ELOC</h2>
+
+<h2>[77] EMC1</h2>
+
+<h2>[78] ERC1</h2>
+
+<h2>[79] ERGIC1</h2>
+
+<h2>[80] ERLEC1</h2>
+
+<h2>[81] ERMP1</h2>
+
+<h2>[82] ERP44</h2>
+
+<h2>[83] EXOSC2</h2>
+
+<h2>[84] EXOSC3</h2>
+
+<h2>[85] EXOSC5</h2>
+
+<h2>[86] EXOSC8</h2>
+
+<h2>[87] F2RL1</h2>
+
+<h2>[88] FAM162A</h2>
+
+<h2>[89] FAM8A1</h2>
+
+<h2>[90] FAM98A</h2>
+
+<h2>[91] FAR2</h2>
+
+<h2>[92] FASTKD5</h2>
+
+<h2>[93] FBLN5</h2>
+
+<h2>[94] FBN1</h2>
+
+<h2>[95] FBN2</h2>
+
+<h2>[96] FBXL12</h2>
+
+<h2>[97] FKBP10</h2>
+
+<h2>[98] FKBP15</h2>
+
+<h2>[99] FKBP7</h2>
+
+<h2>[100] FOXRED2</h2>
+
+<h2>[101] FYCO1</h2>
+
+<h2>[102] G3BP1</h2>
+
+<h2>[103] G3BP2</h2>
+
+<h2>[104] GCC1</h2>
+
+<h2>[105] GCC2</h2>
+
+<h2>[106] GDF15</h2>
+
+<h2>[107] GFER</h2>
+
+<h2>[108] GGCX</h2>
+
+<h2>[109] GGH</h2>
+
+<h2>[110] GHITM</h2>
+
+<h2>[111] GIGYF2</h2>
+
+<h2>[112] GLA</h2>
+
+<h2>[113] GNG5</h2>
+
+<h2>[114] GOLGA2</h2>
+
+<h2>[115] GOLGA3</h2>
+
+<h2>[116] GOLGB1</h2>
+
+<h2>[117] GORASP1</h2>
+
+<h2>[118] GPAA1</h2>
+
+<h2>[119] GPX1</h2>
+
+<h2>[120] GRIPAP1</h2>
+
+<h2>[121] GRPEL1</h2>
+
+<h2>[122] GTF2F2</h2>
+
+<h2>[123] HDAC2</h2>
+
+<h2>[124] HEATR3</h2>
+
+<h2>[125] HECTD1</h2>
+
+<h2>[126] HMOX1</h2>
+
+<h2>[127] HOOK1</h2>
+
+<h2>[128] HS2ST1</h2>
+
+<h2>[129] HS6ST2</h2>
+
+<h2>[130] HYOU1</h2>
+
+<h2>[131] IDE</h2>
+
+<h2>[132] IDE[0-2343]</h2>
+
+<h2>[133] IDE[2342-3240]</h2>
+
+<h2>[134] IDE[3239-4911]</h2>
+
+<h2>[135] IL17RA</h2>
+
+<h2>[136] IMPDH2</h2>
+
+<h2>[137] INHBE</h2>
+
+<h2>[138] ITGB1</h2>
+
+<h2>[139] JAKMIP1</h2>
+
+<h2>[140] LARP1</h2>
+
+<h2>[141] LARP4B</h2>
+
+<h2>[142] LARP7</h2>
+
+<h2>[143] LMAN2</h2>
+
+<h2>[144] LOX</h2>
+
+<h2>[145] MAP7D1</h2>
+
+<h2>[146] MARK1</h2>
+
+<h2>[147] MARK2</h2>
+
+<h2>[148] MARK3</h2>
+
+<h2>[149] MAT2B</h2>
+
+<h2>[150] MDN1</h2>
+
+<h2>[151] MEPCE</h2>
+
+<h2>[152] MFGE8</h2>
+
+<h2>[153] MIB1</h2>
+
+<h2>[154] MIPOL1</h2>
+
+<h2>[155] MOGS</h2>
+
+<h2>[156] MPHOSPH10</h2>
+
+<h2>[157] MRPS2</h2>
+
+<h2>[158] MRPS25</h2>
+
+<h2>[159] MRPS27</h2>
+
+<h2>[160] MRPS5</h2>
+
+<h2>[161] MTCH1</h2>
+
+<h2>[162] MYCBP2</h2>
+
+<h2>[163] NARS2</h2>
+
+<h2>[164] NAT14</h2>
+
+<h2>[165] NDFIP2</h2>
+
+<h2>[166] NDUFAF1</h2>
+
+<h2>[167] NDUFAF2</h2>
+
+<h2>[168] NDUFB9</h2>
+
+<h2>[169] NEK9</h2>
+
+<h2>[170] NEU1</h2>
+
+<h2>[171] NGDN</h2>
+
+<h2>[172] NGLY1</h2>
+
+<h2>[173] NIN</h2>
+
+<h2>[174] NINL</h2>
+
+<h2>[175] NLRX1</h2>
+
+<h2>[176] NOL10</h2>
+
+<h2>[177] NPC2</h2>
+
+<h2>[178] NPTX1</h2>
+
+<h2>[179] NSD2</h2>
+
+<h2>[180] NUP210</h2>
+
+<h2>[181] NUP214</h2>
+
+<h2>[182] NUP54</h2>
+
+<h2>[183] NUP58</h2>
+
+<h2>[184] NUP62</h2>
+
+<h2>[185] NUP88</h2>
+
+<h2>[186] NUP98</h2>
+
+<h2>[187] NUTF2</h2>
+
+<h2>[188] OS9</h2>
+
+<h2>[189] PABPC4</h2>
+
+<h2>[190] PCNT</h2>
+
+<h2>[191] PCSK5</h2>
+
+<h2>[192] PDZD11</h2>
+
+<h2>[193] PIGO</h2>
+
+<h2>[194] PIGS</h2>
+
+<h2>[195] PITRM1</h2>
+
+<h2>[196] PKP2</h2>
+
+<h2>[197] PLAT</h2>
+
+<h2>[198] PLD3</h2>
+
+<h2>[199] PLEKHA5</h2>
+
+<h2>[200] PLEKHF2</h2>
+
+<h2>[201] PLOD2</h2>
+
+<h2>[202] PMPCA</h2>
+
+<h2>[203] PMPCB</h2>
+
+<h2>[204] POFUT1</h2>
+
+<h2>[205] KDELC1</h2>
+
+<h2>[206] KDELC2</h2>
+
+<h2>[207] POLA1</h2>
+
+<h2>[208] POLA2</h2>
+
+<h2>[209] POR</h2>
+
+<h2>[210] PPIL3</h2>
+
+<h2>[211] PPT1</h2>
+
+<h2>[212] PRIM1</h2>
+
+<h2>[213] PRIM2</h2>
+
+<h2>[214] PRKACA</h2>
+
+<h2>[215] PRKAR2A</h2>
+
+<h2>[216] PRKAR2B</h2>
+
+<h2>[217] PRRC2B</h2>
+
+<h2>[218] PSMD8</h2>
+
+<h2>[219] PTBP2</h2>
+
+<h2>[220] PTGES2</h2>
+
+<h2>[221] PTGES2[0-513]</h2>
+
+<h2>[222] PTGES2[512-2070]</h2>
+
+<h2>[223] PUSL1</h2>
+
+<h2>[224] PVR</h2>
+
+<h2>[225] QSOX2</h2>
+
+<h2>[226] RAB10</h2>
+
+<h2>[227] RAB14</h2>
+
+<h2>[228] RAB18</h2>
+
+<h2>[229] RAB1A</h2>
+
+<h2>[230] RAB2A</h2>
+
+<h2>[231] RAB5C</h2>
+
+<h2>[232] RAB7A</h2>
+
+<h2>[233] RAB8A</h2>
+
+<h2>[234] RAE1</h2>
+
+<h2>[235] RALA</h2>
+
+<h2>[236] RAP1GDS1</h2>
+
+<h2>[237] RBM28</h2>
+
+<h2>[238] RBM41</h2>
+
+<h2>[239] RBX1</h2>
+
+<h2>[240] REEP5</h2>
+
+<h2>[241] REEP6</h2>
+
+<h2>[242] RETREG3</h2>
+
+<h2>[243] RHOA</h2>
+
+<h2>[244] RIPK1</h2>
+
+<h2>[245] RNF41</h2>
+
+<h2>[246] RPL36</h2>
+
+<h2>[247] RRP9</h2>
+
+<h2>[248] RTN4</h2>
+
+<h2>[249] SAAL1</h2>
+
+<h2>[250] SBNO1</h2>
+
+<h2>[251] SCAP</h2>
+
+<h2>[252] SCARB1</h2>
+
+<h2>[253] SCARB1[0-2004]</h2>
+
+<h2>[254] SCARB1[2003-2289]</h2>
+
+<h2>[255] SCCPDH</h2>
+
+<h2>[256] SELENOS[0-927]</h2>
+
+<h2>[257] SELENOS[926-1137]</h2>
+
+<h2>[258] SEPSECS</h2>
+
+<h2>[259] SIGMAR1</h2>
+
+<h2>[260] SIL1</h2>
+
+<h2>[261] SIRT5</h2>
+
+<h2>[262] SLC25A21</h2>
+
+<h2>[263] SLC27A2</h2>
+
+<h2>[264] SLC30A6</h2>
+
+<h2>[265] SLC30A7</h2>
+
+<h2>[266] SLC30A9</h2>
+
+<h2>[267] SLC44A2</h2>
+
+<h2>[268] SLC44A2[0-2820]</h2>
+
+<h2>[269] SLC44A2[2819-3792]</h2>
+
+<h2>[270] SLC9A3R1</h2>
+
+<h2>[271] SLU7</h2>
+
+<h2>[272] SMOC1</h2>
+
+<h2>[273] SNIP1</h2>
+
+<h2>[274] SPART</h2>
+
+<h2>[275] SRP19</h2>
+
+<h2>[276] SRP54</h2>
+
+<h2>[277] SRP72</h2>
+
+<h2>[278] STC2</h2>
+
+<h2>[279] STOM</h2>
+
+<h2>[280] STOML2</h2>
+
+<h2>[281] SUN2</h2>
+
+<h2>[282] TAPT1</h2>
+
+<h2>[283] TBK1</h2>
+
+<h2>[284] TBKBP1</h2>
+
+<h2>[285] TCF12</h2>
+
+<h2>[286] THTPA</h2>
+
+<h2>[287] TIMM10</h2>
+
+<h2>[288] TIMM10B</h2>
+
+<h2>[289] TIMM29</h2>
+
+<h2>[290] TIMM8B</h2>
+
+<h2>[291] TIMM9</h2>
+
+<h2>[292] TLE1</h2>
+
+<h2>[293] TLE3</h2>
+
+<h2>[294] TLE5</h2>
+
+<h2>[295] TM2D3</h2>
+
+<h2>[296] TMED5</h2>
+
+<h2>[297] TMEM97</h2>
+
+<h2>[298] TOMM70</h2>
+
+<h2>[299] TOR1A</h2>
+
+<h2>[300] TOR1AIP1</h2>
+
+<h2>[301] TRIM59</h2>
+
+<h2>[302] TRMT1</h2>
+
+<h2>[303] TUBGCP2</h2>
+
+<h2>[304] TUBGCP3</h2>
+
+<h2>[305] UBAP2</h2>
+
+<h2>[306] UBAP2L</h2>
+
+<h2>[307] UBXN8</h2>
+
+<h2>[308] UGGT2</h2>
+
+<h2>[309] UPF1</h2>
+
+<h2>[310] USP13</h2>
+
+<h2>[311] USP54</h2>
+
+<h2>[312] VPS11</h2>
+
+<h2>[313] VPS39</h2>
+
+<h2>[314] WASHC4</h2>
+
+<h2>[315] WFS1</h2>
+
+<h2>[316] YIF1A</h2>
+
+<h2>[317] ZC3H18</h2>
+
+<h2>[318] ZC3H18[0-1101]</h2>
+
+<h2>[319] ZC3H18[1100-3678]</h2>
+
+<h2>[320] ZC3H7A</h2>
+
+<h2>[321] ZDHHC5</h2>
+
+<h2>[322] ZNF318</h2>
+
+<h2>[323] ZNF503</h2>
+
+<h2>[324] ZYG11B</h2>
+
+<h2>[325] ATE1</h2>
+
+<h2>[326] FGFR1OP</h2>
+
+<h2>[327] COL6A1</h2>
+
+<h2>[328] COQ8B</h2>
+
+<h2>[329] CYB5B</h2>
+
+<h2>[330] DDX21</h2>
+
+<h2>[331] ELOB</h2>
+
+<h2>[332] ERO1B</h2>
+
+<h2>[333] ETFA</h2>
+
+<h2>[334] GNB1</h2>
+
+<h2>[335] GOLGA7</h2>
+
+<h2>[336] HSBP1</h2>
+
+<h2>[337] INTS4</h2>
+
+<h2>[338] MOV10</h2>
+
+<h2>[339] MARC1</h2>
+
+<h2>[340] PABPC1</h2>
+
+<h2>[341] PCSK6</h2>
+
+<h2>[342] PDE4DIP</h2>
+
+<h2>[343] RDX</h2>
+
+<h2>[344] REEP6-A</h2>
+
+<h2>[345] REEP6-B</h2>
+
+<h2>[346] SDF2</h2>
+
+<h2>[347] SELENOS</h2>
+
+<h2>[348] TARS2</h2>
+
+<h2>[349] TBCA</h2>
+
+<h2>[350] TMEM39B</h2>
+
+<h2>[351] TMPRSS2</h2>
+
+<h2>[352] TMPRSS2</h2>
+
+<h2>[353] TYSND1</h2>
+
+<h2>352 Levels: AAR2 AASS … REEP6-B</h2>
+
+<p>\end{verbatim}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# genes in common}
+\hlstd{dginnT}\hlopt{\(}\hlstd{Gene.name[dginnT}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name]}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] AAR2 AASS</h2>
+
+<h2>[3] AATF ABCC1</h2>
+
+<h2>[5] ACAD9 ACADM</h2>
+
+<h2>[7] ACE2 ACSL3</h2>
+
+<h2>[9] ADAM9 ADAMTS1</h2>
+
+<h2>[11] AGPS AKAP8</h2>
+
+<h2>[13] AKAP8L AKAP9</h2>
+
+<h2>[15] ALG11 ALG5</h2>
+
+<h2>[17] ALG8 ANO6</h2>
+
+<h2>[19] AP2A2 AP2M1</h2>
+
+<h2>[21] AP3B1 ARF6</h2>
+
+<h2>[23] ATE1 ATP13A3</h2>
+
+<h2>[25] ATP1B1 ATP6AP1</h2>
+
+<h2>[27] ATP6V1A BAG5</h2>
+
+<h2>[29] BCKDK BRD2</h2>
+
+<h2>[31] BRD4 BZW2</h2>
+
+<h2>[33] CCDC86 CDK5RAP2</h2>
+
+<h2>[35] CENPF CEP112</h2>
+
+<h2>[37] CEP135 CEP250</h2>
+
+<h2>[39] CEP350 CEP68</h2>
+
+<h2>[41] CHMP2A CHPF</h2>
+
+<h2>[43] CHPF2 CISD3</h2>
+
+<h2>[45] CIT CLCC1</h2>
+
+<h2>[47] CLIP4 CNTRL</h2>
+
+<h2>[49] COL6A1 COLGALT1</h2>
+
+<h2>[51] COMT COQ8B</h2>
+
+<h2>[53] CRTC3 CSDE1</h2>
+
+<h2>[55] CSNK2A2 CSNK2B</h2>
+
+<h2>[57] CUL2 CWC27</h2>
+
+<h2>[59] CYB5B DCAF7</h2>
+
+<h2>[61] DCAKD DCTPP1</h2>
+
+<h2>[63] DDX10 DDX21</h2>
+
+<h2>[65] DNAJC11 DNAJC19</h2>
+
+<h2>[67] DNMT1 DPH5</h2>
+
+<h2>[69] DPY19L1 ECSIT</h2>
+
+<h2>[71] EDEM3 EIF4E2</h2>
+
+<h2>[73] EIF4H ELOC</h2>
+
+<h2>[75] EMC1 ERC1</h2>
+
+<h2>[77] ERGIC1 ERLEC1</h2>
+
+<h2>[79] ERMP1 ERO1B</h2>
+
+<h2>[81] ERP44 ETFA</h2>
+
+<h2>[83] EXOSC2 EXOSC3</h2>
+
+<h2>[85] EXOSC5 EXOSC8</h2>
+
+<h2>[87] F2RL1 FAM162A</h2>
+
+<h2>[89] FAM8A1 FAM98A</h2>
+
+<h2>[91] FAR2 FASTKD5</h2>
+
+<h2>[93] FBLN5 FBN1</h2>
+
+<h2>[95] FBN2 FBXL12</h2>
+
+<h2>[97] FKBP10 FKBP15</h2>
+
+<h2>[99] FKBP7 FOXRED2</h2>
+
+<h2>[101] FYCO1 G3BP1</h2>
+
+<h2>[103] G3BP2 GCC1</h2>
+
+<h2>[105] GCC2 GDF15</h2>
+
+<h2>[107] GFER GGCX</h2>
+
+<h2>[109] GGH GHITM</h2>
+
+<h2>[111] GIGYF2 GLA</h2>
+
+<h2>[113] GNB1 GNG5</h2>
+
+<h2>[115] GNG5 GOLGA2</h2>
+
+<h2>[117] GOLGA3 GOLGA7</h2>
+
+<h2>[119] GOLGB1 GORASP1</h2>
+
+<h2>[121] GPAA1 GPX1</h2>
+
+<h2>[123] GRIPAP1 GRPEL1</h2>
+
+<h2>[125] GTF2F2 HDAC2</h2>
+
+<h2>[127] HEATR3 HECTD1</h2>
+
+<h2>[129] HMOX1 HOOK1</h2>
+
+<h2>[131] HS2ST1 HS6ST2</h2>
+
+<h2>[133] HSBP1 HYOU1</h2>
+
+<h2>[135] IDE IL17RA</h2>
+
+<h2>[137] IMPDH2 INHBE</h2>
+
+<h2>[139] INTS4 ITGB1</h2>
+
+<h2>[141] JAKMIP1 LARP1</h2>
+
+<h2>[143] LARP4B LARP7</h2>
+
+<h2>[145] LMAN2 LOX</h2>
+
+<h2>[147] MAP7D1 MARK1</h2>
+
+<h2>[149] MARK2 MARK3</h2>
+
+<h2>[151] MAT2B MDN1</h2>
+
+<h2>[153] MEPCE MIB1</h2>
+
+<h2>[155] MIPOL1 MOGS</h2>
+
+<h2>[157] MOV10 MPHOSPH10</h2>
+
+<h2>[159] MRPS2 MRPS25</h2>
+
+<h2>[161] MRPS27 MRPS5</h2>
+
+<h2>[163] MARC1 MTCH1</h2>
+
+<h2>[165] MYCBP2 NARS2</h2>
+
+<h2>[167] NAT14 NDFIP2</h2>
+
+<h2>[169] NDUFAF1 NDUFAF2</h2>
+
+<h2>[171] NDUFB9 NEK9</h2>
+
+<h2>[173] NEU1 NGDN</h2>
+
+<h2>[175] NGLY1 NIN</h2>
+
+<h2>[177] NINL NLRX1</h2>
+
+<h2>[179] NOL10 NPC2</h2>
+
+<h2>[181] NPTX1 NSD2</h2>
+
+<h2>[183] NUP210 NUP214</h2>
+
+<h2>[185] NUP54 NUP58</h2>
+
+<h2>[187] NUP62 NUP88</h2>
+
+<h2>[189] NUP98 NUTF2</h2>
+
+<h2>[191] OS9 PABPC1</h2>
+
+<h2>[193] PABPC4 PCNT</h2>
+
+<h2>[195] PCSK6 PCSK5</h2>
+
+<h2>[197] PDE4DIP PDZD11</h2>
+
+<h2>[199] PIGO PIGS</h2>
+
+<h2>[201] PITRM1 PKP2</h2>
+
+<h2>[203] PLAT PLD3</h2>
+
+<h2>[205] PLEKHA5 PLEKHF2</h2>
+
+<h2>[207] PLOD2 PMPCA</h2>
+
+<h2>[209] PMPCB POFUT1</h2>
+
+<h2>[211] KDELC1 KDELC2</h2>
+
+<h2>[213] POLA1 POLA2</h2>
+
+<h2>[215] POR PPIL3</h2>
+
+<h2>[217] PPT1 PRIM1</h2>
+
+<h2>[219] PRIM2 PRKACA</h2>
+
+<h2>[221] PRKAR2A PRKAR2B</h2>
+
+<h2>[223] PRRC2B PSMD8</h2>
+
+<h2>[225] PTBP2 PTGES2</h2>
+
+<h2>[227] PUSL1 PVR</h2>
+
+<h2>[229] QSOX2 RAB10</h2>
+
+<h2>[231] RAB14 RAB18</h2>
+
+<h2>[233] RAB1A RAB2A</h2>
+
+<h2>[235] RAB5C RAB7A</h2>
+
+<h2>[237] RAB8A RAE1</h2>
+
+<h2>[239] RALA RAP1GDS1</h2>
+
+<h2>[241] RBM28 RBM41</h2>
+
+<h2>[243] RBX1 RDX</h2>
+
+<h2>[245] REEP5 REEP6</h2>
+
+<h2>[247] RETREG3 RHOA</h2>
+
+<h2>[249] RIPK1 RNF41</h2>
+
+<h2>[251] RPL36 RRP9</h2>
+
+<h2>[253] RTN4 SAAL1</h2>
+
+<h2>[255] SBNO1 SCAP</h2>
+
+<h2>[257] SCARB1 SCCPDH</h2>
+
+<h2>[259] SDF2 SEPSECS</h2>
+
+<h2>[261] SIL1 SIRT5</h2>
+
+<h2>[263] SLC25A21 SLC27A2</h2>
+
+<h2>[265] SLC30A6 SLC30A7</h2>
+
+<h2>[267] SLC30A9 SLC44A2</h2>
+
+<h2>[269] SLC9A3R1 SLU7</h2>
+
+<h2>[271] SMOC1 SNIP1</h2>
+
+<h2>[273] SPART SRP19</h2>
+
+<h2>[275] SRP54 SRP72</h2>
+
+<h2>[277] STC2 STOM</h2>
+
+<h2>[279] STOML2 SUN2</h2>
+
+<h2>[281] TAPT1 TARS2</h2>
+
+<h2>[283] TBCA TBK1</h2>
+
+<h2>[285] TBKBP1 TCF12</h2>
+
+<h2>[287] THTPA TIMM10</h2>
+
+<h2>[289] TIMM10B TIMM29</h2>
+
+<h2>[291] TIMM8B TIMM9</h2>
+
+<h2>[293] TLE1 TLE3</h2>
+
+<h2>[295] TM2D3 TMED5</h2>
+
+<h2>[297] TMEM39B TMEM97</h2>
+
+<h2>[299] TMPRSS2 TOMM70</h2>
+
+<h2>[301] TOR1A TOR1AIP1</h2>
+
+<h2>[303] TRIM59 TRMT1</h2>
+
+<h2>[305] TUBGCP2 TUBGCP3</h2>
+
+<h2>[307] TYSND1 UBAP2</h2>
+
+<h2>[309] UBAP2L UBXN8</h2>
+
+<h2>[311] UGGT2 UPF1</h2>
+
+<h2>[313] USP54 VPS11</h2>
+
+<h2>[315] VPS39 WASHC4</h2>
+
+<h2>[317] WFS1 YIF1A</h2>
+
+<h2>[319] ZC3H18 ZC3H7A</h2>
+
+<h2>[321] ZDHHC5 ZNF318</h2>
+
+<h2>[323] ZNF503 ZYG11B</h2>
+
+<h2>[325] RIPK1</h2>
+
+<h2>416 Levels: AAR2 AASS … SELENOS</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{length}\hlstd{(dginnT}\hlopt{\(}\hlstd{Gene.name[dginnT}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name])}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 325</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlcom{# genes only in primates}
+\hlstd{dginnT}\hlopt{\(}\hlstd{Gene.name[(dginnT}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] ADAM9[0-3120]</h2>
+
+<h2>[2] ADAM9[3119-3927]</h2>
+
+<h2>[3] ATP5MGL</h2>
+
+<h2>[4] BCS1L</h2>
+
+<h2>[5] C1H1ORF50</h2>
+
+<h2>[6] CEP135[0-3264]</h2>
+
+<h2>[7] CEP135[3263-3678]</h2>
+
+<h2>[8] CEP43</h2>
+
+<h2>[9] COQ8A</h2>
+
+<h2>[10] CSNK2A1</h2>
+
+<h2>[11] CSNK2B[0-609]</h2>
+
+<h2>[12] CSNK2B[608-2568]</h2>
+
+<h2>[13] CYB5R3</h2>
+
+<h2>[14] CYB5R1</h2>
+
+<h2>[15] DDX21[0-717]</h2>
+
+<h2>[16] DDX21[716-2538]</h2>
+
+<h2>[17] DDX50</h2>
+
+<h2>[18] DNAJC15</h2>
+
+<h2>[19] DPH5[0-702]</h2>
+
+<h2>[20] DPH5[701-1326]</h2>
+
+<h2>[21] DPY19L2</h2>
+
+<h2>[22] EXOSC3[0-1446]</h2>
+
+<h2>[23] EXOSC3[1445-1980]</h2>
+
+<h2>[24] FBN3</h2>
+
+<h2>[25] GNB4</h2>
+
+<h2>[26] GNB2</h2>
+
+<h2>[27] GNB3</h2>
+
+<h2>[28] GOLGA7[0-312]</h2>
+
+<h2>[29] GOLGA7[311-549]</h2>
+
+<h2>[30] GPX1[0-1218]</h2>
+
+<h2>[31] GPX1[1217-2946]</h2>
+
+<h2>[32] HDAC1</h2>
+
+<h2>[33] HS6ST3</h2>
+
+<h2>[34] IMPDH1</h2>
+
+<h2>[35] ITGB1[0-2328]</h2>
+
+<h2>[36] ITGB1[2327-2844]</h2>
+
+<h2>[37] LMAN2L</h2>
+
+<h2>[38] MRPS5[0-1569]</h2>
+
+<h2>[39] MRPS5[1568-3783]</h2>
+
+<h2>[40] MARC2</h2>
+
+<h2>[41] MGRN1</h2>
+
+<h2>[42] NDFIP2[0-768]</h2>
+
+<h2>[43] NDFIP2[767-1314]</h2>
+
+<h2>[44] NDUFAF2[0-258]</h2>
+
+<h2>[45] NDUFAF2[257-744]</h2>
+
+<h2>[46] NUP58[0-1824]</h2>
+
+<h2>[47] NUP58[1823-2367]</h2>
+
+<h2>[48] PABPC3</h2>
+
+<h2>[49] POTPABPC1</h2>
+
+<h2>[50] PABPC4L</h2>
+
+<h2>[51] PABPC5</h2>
+
+<h2>[52] PRIM2[0-1071]</h2>
+
+<h2>[53] PRIM2[1070-1902]</h2>
+
+<h2>[54] PRKACB</h2>
+
+<h2>[55] PRKACG</h2>
+
+<h2>[56] PTGES2[0-1587]</h2>
+
+<h2>[57] PTGES2[1586-2202]</h2>
+
+<h2>[58] RAB8B</h2>
+
+<h2>[59] RAB13</h2>
+
+<h2>[60] RAB18[0-855]</h2>
+
+<h2>[61] RAB18[854-1815]</h2>
+
+<h2>[62] RAB2B</h2>
+
+<h2>[63] RAB5A</h2>
+
+<h2>[64] RAB5B</h2>
+
+<h2>[65] RAB15</h2>
+
+<h2>[66] RALB</h2>
+
+<h2>[67] EZR</h2>
+
+<h2>[68] EZR[0-1458]</h2>
+
+<h2>[69] EZR[1457-3771]</h2>
+
+<h2>[70] MSN</h2>
+
+<h2>[71] RHOB</h2>
+
+<h2>[72] RHOC</h2>
+
+<h2>[73] SLC44A2[0-2577]</h2>
+
+<h2>[74] SLC44A2[2576-3657]</h2>
+
+<h2>[75] SRP72[0-2604]</h2>
+
+<h2>[76] SRP72[2603-3417]</h2>
+
+<h2>[77] STOM[0-1047]</h2>
+
+<h2>[78] STOM[1046-1800]</h2>
+
+<h2>[79] STOML3</h2>
+
+<h2>[80] TLE4</h2>
+
+<h2>[81] TLE2</h2>
+
+<h2>[82] TLE2[0-1302]</h2>
+
+<h2>[83] TLE2[1301-3987]</h2>
+
+<h2>[84] AES</h2>
+
+<h2>[85] TOR1B</h2>
+
+<h2>[86] WFS1[0-2346]</h2>
+
+<h2>[87] WFS1[2345-3216]</h2>
+
+<h2>[88] YIF1B</h2>
+
+<h2>416 Levels: AAR2 AASS … SELENOS</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{length}\hlstd{(dginnT}\hlopt{\(}\hlstd{Gene.name[(dginnT}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 88</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlcom{# genes only in bats}
+\hlstd{dginnbats}\hlopt{\(}\hlstd{Gene.name[(dginnbats}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] ADAM9[0-2769]</h2>
+
+<h2>[2] ADAM9[2768-3030]</h2>
+
+<h2>[3] ARL6IP6</h2>
+
+<h2>[4] ATP5MG</h2>
+
+<h2>[5] BCS1</h2>
+
+<h2>[6] CUNH1ORF50</h2>
+
+<h2>[7] CYB5BR3</h2>
+
+<h2>[8] IDE[0-2343]</h2>
+
+<h2>[9] IDE[2342-3240]</h2>
+
+<h2>[10] IDE[3239-4911]</h2>
+
+<h2>[11] MFGE8</h2>
+
+<h2>[12] PTGES2[0-513]</h2>
+
+<h2>[13] PTGES2[512-2070]</h2>
+
+<h2>[14] SCARB1[0-2004]</h2>
+
+<h2>[15] SCARB1[2003-2289]</h2>
+
+<h2>[16] SELENOS[0-927]</h2>
+
+<h2>[17] SELENOS[926-1137]</h2>
+
+<h2>[18] SIGMAR1</h2>
+
+<h2>[19] SLC44A2[0-2820]</h2>
+
+<h2>[20] SLC44A2[2819-3792]</h2>
+
+<h2>[21] TLE5</h2>
+
+<h2>[22] USP13</h2>
+
+<h2>[23] ZC3H18[0-1101]</h2>
+
+<h2>[24] ZC3H18[1100-3678]</h2>
+
+<h2>[25] FGFR1OP</h2>
+
+<h2>[26] ELOB</h2>
+
+<h2>[27] REEP6-A</h2>
+
+<h2>[28] REEP6-B</h2>
+
+<h2>[29] SELENOS</h2>
+
+<h2>352 Levels: AAR2 AASS … REEP6-B</h2>
+
+<p>\end{verbatim}
+\begin{alltt}
+\hlkwd{length}\hlstd{(dginnbats}\hlopt{\(}\hlstd{Gene.name[(dginnbats}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
+\end{alltt}
+\begin{verbatim}</p>
+
+<h2>[1] 29</h2>
+
+<p>\end{verbatim}
+\end{kframe}
+\end{knitrout}</p>
+
+<p>\end{document}</p>
+
+</body>
+
+</html>
diff --git a/covid_comp_script0_table.pdf b/covid_comp_script0_table.pdf
index 669dd5b72c62078bbb831a30e6085797bff4df95..9676ae3a3d1aa7285328509717f93debf83197cb 100644
Binary files a/covid_comp_script0_table.pdf and b/covid_comp_script0_table.pdf differ
diff --git a/covid_comp_script0_table.tex b/covid_comp_script0_table.tex
index c8b1af626e8cf56061f18834acff7cdbb2a492db..a591a5a6ab05a19bc7a4f2cd1ea6b30b10daa0f9 100644
--- a/covid_comp_script0_table.tex
+++ b/covid_comp_script0_table.tex
@@ -184,36 +184,55 @@
\hlkwd{names}\hlstd{(dginnT)}
\end{alltt}
\begin{verbatim}
-## [1] "File" "Name" "Gene" "GeneSize" "NbSpecies"
-## [6] "omegaM0Bpp" "omegaM0codeml" "BUSTED" "BUSTED.p.value" "MEME.NbSites"
-## [11] "MEME.PSS" "BppM1M2" "BppM1M2.p.value" "BppM1M2.NbSites" "BppM1M2.PSS"
-## [16] "BppM7M8" "BppM7M8.p.value" "BppM7M8.NbSites" "BppM7M8.PSS" "codemlM1M2"
-## [21] "codemlM1M2.p.value" "codemlM1M2.NbSites" "codemlM1M2.PSS" "codemlM7M8" "codemlM7M8.p.value"
-## [26] "codemlM7M8.NbSites" "codemlM7M8.PSS"
+## [1] "File" "Name" "Gene"
+## [4] "GeneSize" "NbSpecies" "omegaM0Bpp"
+## [7] "omegaM0codeml" "BUSTED" "BUSTED.p.value"
+## [10] "MEME.NbSites" "MEME.PSS" "BppM1M2"
+## [13] "BppM1M2.p.value" "BppM1M2.NbSites" "BppM1M2.PSS"
+## [16] "BppM7M8" "BppM7M8.p.value" "BppM7M8.NbSites"
+## [19] "BppM7M8.PSS" "codemlM1M2" "codemlM1M2.p.value"
+## [22] "codemlM1M2.NbSites" "codemlM1M2.PSS" "codemlM7M8"
+## [25] "codemlM7M8.p.value" "codemlM7M8.NbSites" "codemlM7M8.PSS"
\end{verbatim}
\begin{alltt}
\hlcom{# Number of genes in dginn-primate output not present in the original table}
\hlstd{dginnT[(dginnT}\hlopt{$}\hlstd{Gene} \hlopt{%in%} \hlstd{tab}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlstd{F,}\hlstr{"Gene"}\hlstd{]}
\end{alltt}
\begin{verbatim}
-## [1] ACE2 ADAM9[0-3120] ADAM9[3119-3927] ATP5MGL C1H1ORF50 CEP135[0-3264]
-## [7] CEP135[3263-3678] CEP43 COQ8B COQ8A CSNK2A1 CSNK2B[0-609]
-## [13] CSNK2B[608-2568] CYB5R1 DDX21[0-717] DDX21[716-2538] DDX50 DNAJC15
-## [19] DPH5[0-702] DPH5[701-1326] DPY19L2 ELOC ERO1B EXOSC3[0-1446]
-## [25] EXOSC3[1445-1980] FBN3 GNB4 GNB2 GNB3 GOLGA7[0-312]
-## [31] GOLGA7[311-549] GPX1[0-1218] GPX1[1217-2946] HDAC1 HS6ST3 IMPDH1
-## [37] ITGB1[0-2328] ITGB1[2327-2844] LMAN2L MRPS5[0-1569] MRPS5[1568-3783] MARC2
-## [43] MGRN1 NDFIP2[0-768] NDFIP2[767-1314] NDUFAF2[0-258] NDUFAF2[257-744] NSD2
-## [49] NUP58 NUP58[0-1824] NUP58[1823-2367] PABPC3 POTPABPC1 PABPC4L
-## [55] PABPC5 PCSK5 PRIM2[0-1071] PRIM2[1070-1902] PRKACB PRKACG
-## [61] PTGES2[0-1587] PTGES2[1586-2202] RAB8B RAB13 RAB18[0-855] RAB18[854-1815]
-## [67] RAB2B RAB5A RAB5B RAB15 RALB EZR
-## [73] EZR[0-1458] EZR[1457-3771] MSN RETREG3 RHOB RHOC
-## [79] SLC44A2[0-2577] SLC44A2[2576-3657] SPART SRP72[0-2604] SRP72[2603-3417] STOM[0-1047]
-## [85] STOM[1046-1800] STOML3 TIMM29 TLE4 TLE2 TLE2[0-1302]
-## [91] TLE2[1301-3987] TMPRSS2 TOMM70 TOR1B WASHC4 WFS1[0-2346]
+## [1] ACE2 ADAM9[0-3120] ADAM9[3119-3927]
+## [4] ATP5MGL C1H1ORF50 CEP135[0-3264]
+## [7] CEP135[3263-3678] CEP43 COQ8B
+## [10] COQ8A CSNK2A1 CSNK2B[0-609]
+## [13] CSNK2B[608-2568] CYB5R1 DDX21[0-717]
+## [16] DDX21[716-2538] DDX50 DNAJC15
+## [19] DPH5[0-702] DPH5[701-1326] DPY19L2
+## [22] ELOC ERO1B EXOSC3[0-1446]
+## [25] EXOSC3[1445-1980] FBN3 GNB4
+## [28] GNB2 GNB3 GOLGA7[0-312]
+## [31] GOLGA7[311-549] GPX1[0-1218] GPX1[1217-2946]
+## [34] HDAC1 HS6ST3 IMPDH1
+## [37] ITGB1[0-2328] ITGB1[2327-2844] LMAN2L
+## [40] MRPS5[0-1569] MRPS5[1568-3783] MARC2
+## [43] MGRN1 NDFIP2[0-768] NDFIP2[767-1314]
+## [46] NDUFAF2[0-258] NDUFAF2[257-744] NSD2
+## [49] NUP58 NUP58[0-1824] NUP58[1823-2367]
+## [52] PABPC3 POTPABPC1 PABPC4L
+## [55] PABPC5 PCSK5 PRIM2[0-1071]
+## [58] PRIM2[1070-1902] PRKACB PRKACG
+## [61] PTGES2[0-1587] PTGES2[1586-2202] RAB8B
+## [64] RAB13 RAB18[0-855] RAB18[854-1815]
+## [67] RAB2B RAB5A RAB5B
+## [70] RAB15 RALB EZR
+## [73] EZR[0-1458] EZR[1457-3771] MSN
+## [76] RETREG3 RHOB RHOC
+## [79] SLC44A2[0-2577] SLC44A2[2576-3657] SPART
+## [82] SRP72[0-2604] SRP72[2603-3417] STOM[0-1047]
+## [85] STOM[1046-1800] STOML3 TIMM29
+## [88] TLE4 TLE2 TLE2[0-1302]
+## [91] TLE2[1301-3987] TMPRSS2 TOMM70
+## [94] TOR1B WASHC4 WFS1[0-2346]
## [97] WFS1[2345-3216] YIF1B
-## 411 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ADAM9 ADAM9[0-3120] ADAM9[3119-3927] ADAMTS1 AES AGPS AKAP8 ... ZYG11B
+## 411 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ... ZYG11B
\end{verbatim}
\begin{alltt}
\hlcom{# This includes paralogs, recombinations found by DGINN and additionnal genes }
@@ -223,8 +242,10 @@
\hlstd{tab[(tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlstd{F,}\hlstr{"Gene.name"}\hlstd{]}
\end{alltt}
\begin{verbatim}
-## [1] "ADCK4" "ARL6IP6" "ATP5L" "C19orf52" "C1orf50" "ERO1LB" "FAM134C" "FGFR1OP" "KIAA1033" "MFGE8" "NUPL1"
-## [12] "SIGMAR1" "SPG20" "TCEB1" "TCEB2" "TOMM70A" "USP13" "VIMP" "WHSC1"
+## [1] "ADCK4" "ARL6IP6" "ATP5L" "C19orf52" "C1orf50" "ERO1LB"
+## [7] "FAM134C" "FGFR1OP" "KIAA1033" "MFGE8" "NUPL1" "SIGMAR1"
+## [13] "SPG20" "TCEB1" "TCEB2" "TOMM70A" "USP13" "VIMP"
+## [19] "WHSC1"
\end{verbatim}
\begin{alltt}
\hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"Name"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{,} \hlstr{"GeneSize"}\hlstd{,}
@@ -244,13 +265,78 @@
\end{kframe}
\end{knitrout}
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{$}\hlstd{`dginn-primate_BUSTED`)}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2`)}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8`)}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{$}\hlstd{`dginn-primate_BppM1M2`)}
+\hlkwd{table}\hlstd{(dginnT}\hlopt{$}\hlstd{`dginn-primate_BppM7M8`)}
+
+\hlkwd{table}\hlstd{(dginnT}\hlopt{$}\hlstd{`dginn-primate_BUSTED`}\hlopt{==}\hlstr{"na"}\hlstd{,dginnT}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2`}\hlopt{==}\hlstr{"na"}\hlstd{, dginnT}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8`}\hlopt{==}\hlstr{"na"}\hlstd{,}
+ \hlstd{dginnT}\hlopt{$}\hlstd{`dginn-primate_BppM1M2`}\hlopt{==}\hlstr{"na"}\hlstd{, dginnT}\hlopt{$}\hlstd{`dginn-primate_BppM7M8`}\hlopt{==}\hlstr{"na"} \hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+
\subsection{Join Table and DGINN table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnT,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
+
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BUSTED`)}
+\end{alltt}
+\begin{verbatim}
+##
+## N na Y
+## 155 12 147
+\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2`)}
+\end{alltt}
+\begin{verbatim}
+##
+## N na Y
+## 216 26 72
+\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8`)}
+\end{alltt}
+\begin{verbatim}
+##
+## N na Y
+## 161 40 113
+\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BppM1M2`)}
+\end{alltt}
+\begin{verbatim}
+##
+## N na Y
+## 252 21 41
+\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8`)}
+\end{alltt}
+\begin{verbatim}
+##
+## N na Y
+## 173 22 119
+\end{verbatim}
+\begin{alltt}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BUSTED`}\hlopt{==}\hlstr{"na"} \hlopt{|} \hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2`}\hlopt{==}\hlstr{"na"} \hlopt{|} \hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8`}\hlopt{==}\hlstr{"na"} \hlopt{|}
+ \hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BppM1M2`}\hlopt{==}\hlstr{"na"}\hlopt{|} \hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8`}\hlopt{==}\hlstr{"na"} \hlstd{)}
\end{alltt}
+\begin{verbatim}
+##
+## FALSE TRUE
+## 274 40
+\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -275,7 +361,6 @@ DGINN results from different analysis.
\hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
\hlcom{# colomne choice, BUSTED and Bppml form first file, codeml from the other one}
-
\hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew1}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{omegaM0codeml}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{omegaM0codeml}
@@ -406,13 +491,20 @@ DGINN results from different analysis.
\hlkwd{names}\hlstd{(dginnbats)}
\end{alltt}
\begin{verbatim}
-## [1] "File" "bats_Name" "cooper.batsGene" "bats_GeneSize"
-## [5] "bats_NbSpecies" "bats_omegaM0Bpp" "bats_omegaM0codeml" "bats_BUSTED"
-## [9] "bats_BUSTED.p.value" "bats_MEME.NbSites" "bats_MEME.PSS" "bats_BppM1M2"
-## [13] "bats_BppM1M2.p.value" "bats_BppM1M2.NbSites" "bats_BppM1M2.PSS" "bats_BppM7M8"
-## [17] "bats_BppM7M8.p.value" "bats_BppM7M8.NbSites" "bats_BppM7M8.PSS" "bats_codemlM1M2"
-## [21] "bats_codemlM1M2.p.value" "bats_codemlM1M2.NbSites" "bats_codemlM1M2.PSS" "bats_codemlM7M8"
-## [25] "bats_codemlM7M8.p.value" "bats_codemlM7M8.NbSites" "bats_codemlM7M8.PSS"
+## [1] "File" "bats_Name"
+## [3] "cooper.batsGene" "bats_GeneSize"
+## [5] "bats_NbSpecies" "bats_omegaM0Bpp"
+## [7] "bats_omegaM0codeml" "bats_BUSTED"
+## [9] "bats_BUSTED.p.value" "bats_MEME.NbSites"
+## [11] "bats_MEME.PSS" "bats_BppM1M2"
+## [13] "bats_BppM1M2.p.value" "bats_BppM1M2.NbSites"
+## [15] "bats_BppM1M2.PSS" "bats_BppM7M8"
+## [17] "bats_BppM7M8.p.value" "bats_BppM7M8.NbSites"
+## [19] "bats_BppM7M8.PSS" "bats_codemlM1M2"
+## [21] "bats_codemlM1M2.p.value" "bats_codemlM1M2.NbSites"
+## [23] "bats_codemlM1M2.PSS" "bats_codemlM7M8"
+## [25] "bats_codemlM7M8.p.value" "bats_codemlM7M8.NbSites"
+## [27] "bats_codemlM7M8.PSS"
\end{verbatim}
\begin{alltt}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnbats,} \hlkwc{by}\hlstd{=}\hlstr{"cooper.batsGene"}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
@@ -430,5 +522,744 @@ DGINN results from different analysis.
\end{kframe}
\end{knitrout}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+\section{Second Table}
+
+Table containing the DGINN results for both Primates and bats. Conserve all genes.
+
+\subsection{Primates}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnT}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{"data/DGINN_202005281649summary_cleaned.csv"}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{","}\hlstd{)}
+
+\hlkwd{dim}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}
+## [1] 412 27
+\end{verbatim}
+\begin{alltt}
+\hlkwd{names}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}
+## [1] "File" "Name" "Gene"
+## [4] "GeneSize" "NbSpecies" "omegaM0Bpp"
+## [7] "omegaM0codeml" "BUSTED" "BUSTED.p.value"
+## [10] "MEME.NbSites" "MEME.PSS" "BppM1M2"
+## [13] "BppM1M2.p.value" "BppM1M2.NbSites" "BppM1M2.PSS"
+## [16] "BppM7M8" "BppM7M8.p.value" "BppM7M8.NbSites"
+## [19] "BppM7M8.PSS" "codemlM1M2" "codemlM1M2.p.value"
+## [22] "codemlM1M2.NbSites" "codemlM1M2.PSS" "codemlM7M8"
+## [25] "codemlM7M8.p.value" "codemlM7M8.NbSites" "codemlM7M8.PSS"
+\end{verbatim}
+\begin{alltt}
+\hlcom{# Rename the columns to include primate}
+\hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"Name"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{,} \hlstr{"GeneSize"}\hlstd{,}
+ \hlstr{"dginn-primate_NbSpecies"}\hlstd{,} \hlstr{"dginn-primate_omegaM0Bpp"}\hlstd{,}
+ \hlstr{"dginn-primate_omegaM0codeml"}\hlstd{,} \hlstr{"dginn-primate_BUSTED"}\hlstd{,}
+ \hlstr{"dginn-primate_BUSTED.p.value"}\hlstd{,} \hlstr{"dginn-primate_MEME.NbSites"}\hlstd{,}
+ \hlstr{"dginn-primate_MEME.PSS"}\hlstd{,} \hlstr{"dginn-primate_BppM1M2"}\hlstd{,}
+ \hlstr{"dginn-primate_BppM1M2.p.value"}\hlstd{,} \hlstr{"dginn-primate_BppM1M2.NbSites"}\hlstd{,}
+ \hlstr{"dginn-primate_BppM1M2.PSS"}\hlstd{,} \hlstr{"dginn-primate_BppM7M8"}\hlstd{,}
+ \hlstr{"dginn-primate_BppM7M8.p.value"}\hlstd{,} \hlstr{"dginn-primate_BppM7M8.NbSites"}\hlstd{,}
+ \hlstr{"dginn-primate_BppM7M8.PSS"}\hlstd{,} \hlstr{"dginn-primate_codemlM1M2"}\hlstd{,}
+ \hlstr{"dginn-primate_codemlM1M2.p.value"}\hlstd{,} \hlstr{"dginn-primate_codemlM1M2.NbSites"}\hlstd{,}
+ \hlstr{"dginn-primate_codemlM1M2.PSS"}\hlstd{,} \hlstr{"dginn-primate_codemlM7M8"}\hlstd{,}
+ \hlstr{"dginn-primate_codemlM7M8.p.value"}\hlstd{,} \hlstr{"dginn-primate_codemlM7M8.NbSites"}\hlstd{,}
+ \hlstr{"dginn-primate_codemlM7M8.PSS"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\subsection{Bats}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# original table}
+\hlstd{dginnbats}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{"data/DGINN_202005281339summary_cleaned-LE201108.txt"}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
+
+\hlcom{# rerun on corrected alignment}
+\hlstd{dginnbatsnew}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{"data/DGINN_202011262248_hyphybpp-202012192053_codeml-summary.txt"}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Add both columns }
+\hlstd{dginnbatsnew}\hlopt{$}\hlstd{Lucie.s.comments}\hlkwb{<-}\hlstr{""}
+\hlstd{dginnbatsnew}\hlopt{$}\hlstd{Action.taken}\hlkwb{<-}\hlstr{""}
+
+\hlcom{# Homogenize column names}
+\hlstd{dginnbats}\hlopt{$}\hlstd{BUSTED_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{BUSTED.p.value}
+\hlstd{dginnbats}\hlopt{$}\hlstd{MEME_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{MEME.NbSites}
+\hlstd{dginnbats}\hlopt{$}\hlstd{MEME_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{MEME.PSS}
+
+\hlstd{dginnbats}\hlopt{$}\hlstd{BppM1M2_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{BppM1M2.p.value}
+\hlstd{dginnbats}\hlopt{$}\hlstd{BppM1M2_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{BppM1M2.NbSites}
+\hlstd{dginnbats}\hlopt{$}\hlstd{BppM1M2_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{BppM1M2.PSS}
+
+\hlstd{dginnbats}\hlopt{$}\hlstd{BppM7M8_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{BppM7M8.p.value}
+\hlstd{dginnbats}\hlopt{$}\hlstd{BppM7M8_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{BppM7M8.NbSites}
+\hlstd{dginnbats}\hlopt{$}\hlstd{BppM7M8_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{BppM7M8.PSS}
+
+\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM1M2_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM1M2.p.value}
+\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM1M2_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM1M2.NbSites}
+\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM1M2_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM1M2.PSS}
+
+\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM7M8_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM7M8.p.value}
+\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM7M8_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM7M8.NbSites}
+\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM7M8_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{codemlM7M8.PSS}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Order columns in the same order in both tables}
+\hlstd{dginnbats}\hlkwb{<-}\hlstd{dginnbats[,}\hlkwd{names}\hlstd{(dginnbatsnew)]}
+
+\hlkwd{names}\hlstd{(dginnbatsnew)} \hlopt{%in%} \hlkwd{names}\hlstd{(dginnbats)}
+\end{alltt}
+\begin{verbatim}
+## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+## [14] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+## [27] TRUE TRUE TRUE
+\end{verbatim}
+\begin{alltt}
+\hlkwd{names}\hlstd{(dginnbats)}\hlopt{==}\hlkwd{names}\hlstd{(dginnbatsnew)}
+\end{alltt}
+\begin{verbatim}
+## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+## [14] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+## [27] TRUE TRUE TRUE
+\end{verbatim}
+\begin{alltt}
+\hlcom{# Put RIPK aside}
+\hlstd{ripk1}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlnum{1}\hlopt{:}\hlnum{27}\hlstd{]}
+
+\hlcom{# Add it to primate table}
+\hlkwd{names}\hlstd{(ripk1)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnT)}
+
+\hlstd{ripk1}\hlopt{$}\hlstd{`dginn-primate_omegaM0Bpp`}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{$}\hlstd{`dginn-primate_omegaM0Bpp`)}
+\hlstd{ripk1}\hlopt{$}\hlstd{`dginn-primate_BUSTED.p.value`}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{$}\hlstd{`dginn-primate_BUSTED.p.value`)}
+\hlstd{ripk1}\hlopt{$}\hlstd{`dginn-primate_BppM1M2.p.value`}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{$}\hlstd{`dginn-primate_BppM1M2.p.value`)}
+\hlstd{ripk1}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.p.value`}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.p.value`)}
+
+\hlstd{dginnT}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnT, ripk1)}
+
+\hlcom{## Remove it Ripk1 from bats}
+\hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{!=}\hlstr{"RIPK1"}\hlstd{,]}
+
+
+\hlcom{## suppress redundant lines}
+\hlstd{dginnbats}\hlkwb{<-}\hlstd{dginnbats[(dginnbats}\hlopt{$}\hlstd{Gene} \hlopt{%in%} \hlstd{dginnbatsnew}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlnum{FALSE}\hlstd{,]}
+\hlkwd{names}\hlstd{(dginnbatsnew)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnbats)}
+
+\hlcom{## replace by new data}
+\hlstd{dginnbatsnew}\hlopt{$}\hlstd{omegaM0Bpp}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(dginnbatsnew}\hlopt{$}\hlstd{omegaM0Bpp)}
+\hlstd{dginnbatsnew}\hlopt{$}\hlstd{BppM1M2_p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(dginnbatsnew}\hlopt{$}\hlstd{BppM1M2_p.value)}
+\hlstd{dginnbatsnew}\hlopt{$}\hlstd{BppM7M8_p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(dginnbatsnew}\hlopt{$}\hlstd{BppM7M8_p.value)}
+
+\hlstd{dginnbats}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnbats, dginnbatsnew)}
+
+\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"bats_File"}\hlstd{,} \hlstr{"bats_Name"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{"bats_"}\hlstd{,}
+ \hlkwd{names}\hlstd{(dginnbats)[}\hlopt{-}\hlstd{(}\hlnum{1}\hlopt{:}\hlnum{3}\hlstd{)]))}
+\hlkwd{names}\hlstd{(dginnbats)}
+\end{alltt}
+\begin{verbatim}
+## [1] "bats_File" "bats_Name"
+## [3] "Gene.name" "bats_GeneSize"
+## [5] "bats_NbSpecies" "bats_omegaM0Bpp"
+## [7] "bats_omegaM0codeml" "bats_BUSTED"
+## [9] "bats_BUSTED_p.value" "bats_MEME_NbSites"
+## [11] "bats_MEME_PSS" "bats_BppM1M2"
+## [13] "bats_BppM1M2_p.value" "bats_BppM1M2_NbSites"
+## [15] "bats_BppM1M2_PSS" "bats_BppM7M8"
+## [17] "bats_BppM7M8_p.value" "bats_BppM7M8_NbSites"
+## [19] "bats_BppM7M8_PSS" "bats_codemlM1M2"
+## [21] "bats_codemlM1M2_p.value" "bats_codemlM1M2_NbSites"
+## [23] "bats_codemlM1M2_PSS" "bats_codemlM7M8"
+## [25] "bats_codemlM7M8_p.value" "bats_codemlM7M8_NbSites"
+## [27] "bats_codemlM7M8_PSS" "bats_Lucie.s.comments"
+## [29] "bats_Action.taken"
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+\subsection{Merged table}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{#tidy.opts = list(width.cutoff = 60)}
+\hlkwd{dim}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}
+## [1] 413 27
+\end{verbatim}
+\begin{alltt}
+\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name}
+\end{alltt}
+\begin{verbatim}
+## [1] AAR2 AASS AATF
+## [4] ABCC1 ACAD9 ACADM
+## [7] ACE2 ACSL3 ADAM9
+## [10] ADAM9[0-3120] ADAM9[3119-3927] ADAMTS1
+## [13] AGPS AKAP8 AKAP8L
+## [16] AKAP9 ALG11 ALG5
+## [19] ALG8 ANO6 AP2A2
+## [22] AP2M1 AP3B1 ARF6
+## [25] ATE1 ATP13A3 ATP1B1
+## [28] ATP5MGL ATP6AP1 ATP6V1A
+## [31] BAG5 BCKDK BCS1L
+## [34] BRD2 BRD4 BZW2
+## [37] C1H1ORF50 CCDC86 CDK5RAP2
+## [40] CENPF CEP112 CEP135
+## [43] CEP135[0-3264] CEP135[3263-3678] CEP250
+## [46] CEP350 CEP43 CEP68
+## [49] CHMP2A CHPF CHPF2
+## [52] CISD3 CIT CLCC1
+## [55] CLIP4 CNTRL COL6A1
+## [58] COLGALT1 COMT COQ8B
+## [61] COQ8A CRTC3 CSDE1
+## [64] CSNK2A1 CSNK2A2 CSNK2B
+## [67] CSNK2B[0-609] CSNK2B[608-2568] CUL2
+## [70] CWC27 CYB5B CYB5R3
+## [73] CYB5R1 DCAF7 DCAKD
+## [76] DCTPP1 DDX10 DDX21
+## [79] DDX21[0-717] DDX21[716-2538] DDX50
+## [82] DNAJC11 DNAJC19 DNAJC15
+## [85] DNMT1 DPH5 DPH5[0-702]
+## [88] DPH5[701-1326] DPY19L2 DPY19L1
+## [91] ECSIT EDEM3 EIF4E2
+## [94] EIF4H ELOC EMC1
+## [97] ERC1 ERGIC1 ERLEC1
+## [100] ERMP1 ERO1B ERP44
+## [103] ETFA EXOSC2 EXOSC3
+## [106] EXOSC3[0-1446] EXOSC3[1445-1980] EXOSC5
+## [109] EXOSC8 F2RL1 FAM162A
+## [112] FAM8A1 FAM98A FAR2
+## [115] FASTKD5 FBLN5 FBN1
+## [118] FBN3 FBN2 FBXL12
+## [121] FKBP10 FKBP15 FKBP7
+## [124] FOXRED2 FYCO1 G3BP1
+## [127] G3BP2 GCC1 GCC2
+## [130] GDF15 GFER GGCX
+## [133] GGH GHITM GIGYF2
+## [136] GLA GNB4 GNB2
+## [139] GNB1 GNB3 GNG5
+## [142] GNG5 GOLGA2 GOLGA3
+## [145] GOLGA7 GOLGA7[0-312] GOLGA7[311-549]
+## [148] GOLGB1 GORASP1 GPAA1
+## [151] GPX1 GPX1[0-1218] GPX1[1217-2946]
+## [154] GRIPAP1 GRPEL1 GTF2F2
+## [157] HDAC2 HDAC1 HEATR3
+## [160] HECTD1 HMOX1 HOOK1
+## [163] HS2ST1 HS6ST2 HS6ST3
+## [166] HSBP1 HYOU1 IDE
+## [169] IL17RA IMPDH1 IMPDH2
+## [172] INHBE INTS4 ITGB1
+## [175] ITGB1[0-2328] ITGB1[2327-2844] JAKMIP1
+## [178] LARP1 LARP4B LARP7
+## [181] LMAN2 LMAN2L LOX
+## [184] MAP7D1 MARK1 MARK2
+## [187] MARK3 MAT2B MDN1
+## [190] MEPCE MIB1 MIPOL1
+## [193] MOGS MOV10 MPHOSPH10
+## [196] MRPS2 MRPS25 MRPS27
+## [199] MRPS5 MRPS5[0-1569] MRPS5[1568-3783]
+## [202] MARC1 MARC2 MTCH1
+## [205] MYCBP2 MGRN1 NARS2
+## [208] NAT14 NDFIP2 NDFIP2[0-768]
+## [211] NDFIP2[767-1314] NDUFAF1 NDUFAF2
+## [214] NDUFAF2[0-258] NDUFAF2[257-744] NDUFB9
+## [217] NEK9 NEU1 NGDN
+## [220] NGLY1 NIN NINL
+## [223] NLRX1 NOL10 NPC2
+## [226] NPTX1 NSD2 NUP210
+## [229] NUP214 NUP54 NUP58
+## [232] NUP58[0-1824] NUP58[1823-2367] NUP62
+## [235] NUP88 NUP98 NUTF2
+## [238] OS9 PABPC3 POTPABPC1
+## [241] PABPC1 PABPC4 PABPC4L
+## [244] PABPC5 PCNT PCSK6
+## [247] PCSK5 PDE4DIP PDZD11
+## [250] PIGO PIGS PITRM1
+## [253] PKP2 PLAT PLD3
+## [256] PLEKHA5 PLEKHF2 PLOD2
+## [259] PMPCA PMPCB POFUT1
+## [262] KDELC1 KDELC2 POLA1
+## [265] POLA2 POR PPIL3
+## [268] PPT1 PRIM1 PRIM2
+## [271] PRIM2[0-1071] PRIM2[1070-1902] PRKACB
+## [274] PRKACG PRKACA PRKAR2A
+## [277] PRKAR2B PRRC2B PSMD8
+## [280] PTBP2 PTGES2 PTGES2[0-1587]
+## [283] PTGES2[1586-2202] PUSL1 PVR
+## [286] QSOX2 RAB10 RAB8B
+## [289] RAB13 RAB14 RAB18
+## [292] RAB18[0-855] RAB18[854-1815] RAB1A
+## [295] RAB2B RAB2A RAB5C
+## [298] RAB5A RAB5B RAB7A
+## [301] RAB15 RAB8A RAE1
+## [304] RALB RALA RAP1GDS1
+## [307] RBM28 RBM41 RBX1
+## [310] EZR EZR[0-1458] EZR[1457-3771]
+## [313] RDX MSN REEP5
+## [316] REEP6 RETREG3 RHOB
+## [319] RHOC RHOA RIPK1
+## [322] RNF41 RPL36 RRP9
+## [325] RTN4 SAAL1 SBNO1
+## [328] SCAP SCARB1 SCCPDH
+## [331] SDF2 SEPSECS SIL1
+## [334] SIRT5 SLC25A21 SLC27A2
+## [337] SLC30A6 SLC30A7 SLC30A9
+## [340] SLC44A2 SLC44A2[0-2577] SLC44A2[2576-3657]
+## [343] SLC9A3R1 SLU7 SMOC1
+## [346] SNIP1 SPART SRP19
+## [349] SRP54 SRP72 SRP72[0-2604]
+## [352] SRP72[2603-3417] STC2 STOM
+## [355] STOM[0-1047] STOM[1046-1800] STOML3
+## [358] STOML2 SUN2 TAPT1
+## [361] TARS2 TBCA TBK1
+## [364] TBKBP1 TCF12 THTPA
+## [367] TIMM10 TIMM10B TIMM29
+## [370] TIMM8B TIMM9 TLE1
+## [373] TLE3 TLE4 TLE2
+## [376] TLE2[0-1302] TLE2[1301-3987] AES
+## [379] TM2D3 TMED5 TMEM39B
+## [382] TMEM97 TMPRSS2 TOMM70
+## [385] TOR1A TOR1B TOR1AIP1
+## [388] TRIM59 TRMT1 TUBGCP2
+## [391] TUBGCP3 TYSND1 UBAP2
+## [394] UBAP2L UBXN8 UGGT2
+## [397] UPF1 USP54 VPS11
+## [400] VPS39 WASHC4 WFS1
+## [403] WFS1[0-2346] WFS1[2345-3216] YIF1A
+## [406] YIF1B ZC3H18 ZC3H7A
+## [409] ZDHHC5 ZNF318 ZNF503
+## [412] ZYG11B RIPK1
+## 416 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ... SELENOS
+\end{verbatim}
+\begin{alltt}
+\hlkwd{dim}\hlstd{(dginnbats)}
+\end{alltt}
+\begin{verbatim}
+## [1] 353 29
+\end{verbatim}
+\begin{alltt}
+\hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name}
+\end{alltt}
+\begin{verbatim}
+## [1] AAR2 AASS AATF
+## [4] ABCC1 ACAD9 ACADM
+## [7] ACE2 ACSL3 ADAM9
+## [10] ADAM9[0-2769] ADAM9[2768-3030] ADAMTS1
+## [13] AGPS AKAP8 AKAP8L
+## [16] AKAP9 ALG11 ALG5
+## [19] ALG8 ANO6 AP2A2
+## [22] AP2M1 AP3B1 ARF6
+## [25] ARL6IP6 ATP13A3 ATP1B1
+## [28] ATP5MG ATP6AP1 ATP6V1A
+## [31] BAG5 BCKDK BCS1
+## [34] BRD2 BRD4 BZW2
+## [37] CUNH1ORF50 CCDC86 CDK5RAP2
+## [40] CENPF CEP112 CEP135
+## [43] CEP250 CEP350 CEP68
+## [46] CHMP2A CHPF CHPF2
+## [49] CISD3 CIT CLCC1
+## [52] CLIP4 CNTRL COLGALT1
+## [55] COMT CRTC3 CSDE1
+## [58] CSNK2A2 CSNK2B CUL2
+## [61] CWC27 CYB5BR3 DCAF7
+## [64] DCAKD DCTPP1 DDX10
+## [67] DNAJC11 DNAJC19 DNMT1
+## [70] DPH5 DPY19L1 ECSIT
+## [73] EDEM3 EIF4E2 EIF4H
+## [76] ELOC EMC1 ERC1
+## [79] ERGIC1 ERLEC1 ERMP1
+## [82] ERP44 EXOSC2 EXOSC3
+## [85] EXOSC5 EXOSC8 F2RL1
+## [88] FAM162A FAM8A1 FAM98A
+## [91] FAR2 FASTKD5 FBLN5
+## [94] FBN1 FBN2 FBXL12
+## [97] FKBP10 FKBP15 FKBP7
+## [100] FOXRED2 FYCO1 G3BP1
+## [103] G3BP2 GCC1 GCC2
+## [106] GDF15 GFER GGCX
+## [109] GGH GHITM GIGYF2
+## [112] GLA GNG5 GOLGA2
+## [115] GOLGA3 GOLGB1 GORASP1
+## [118] GPAA1 GPX1 GRIPAP1
+## [121] GRPEL1 GTF2F2 HDAC2
+## [124] HEATR3 HECTD1 HMOX1
+## [127] HOOK1 HS2ST1 HS6ST2
+## [130] HYOU1 IDE IDE[0-2343]
+## [133] IDE[2342-3240] IDE[3239-4911] IL17RA
+## [136] IMPDH2 INHBE ITGB1
+## [139] JAKMIP1 LARP1 LARP4B
+## [142] LARP7 LMAN2 LOX
+## [145] MAP7D1 MARK1 MARK2
+## [148] MARK3 MAT2B MDN1
+## [151] MEPCE MFGE8 MIB1
+## [154] MIPOL1 MOGS MPHOSPH10
+## [157] MRPS2 MRPS25 MRPS27
+## [160] MRPS5 MTCH1 MYCBP2
+## [163] NARS2 NAT14 NDFIP2
+## [166] NDUFAF1 NDUFAF2 NDUFB9
+## [169] NEK9 NEU1 NGDN
+## [172] NGLY1 NIN NINL
+## [175] NLRX1 NOL10 NPC2
+## [178] NPTX1 NSD2 NUP210
+## [181] NUP214 NUP54 NUP58
+## [184] NUP62 NUP88 NUP98
+## [187] NUTF2 OS9 PABPC4
+## [190] PCNT PCSK5 PDZD11
+## [193] PIGO PIGS PITRM1
+## [196] PKP2 PLAT PLD3
+## [199] PLEKHA5 PLEKHF2 PLOD2
+## [202] PMPCA PMPCB POFUT1
+## [205] KDELC1 KDELC2 POLA1
+## [208] POLA2 POR PPIL3
+## [211] PPT1 PRIM1 PRIM2
+## [214] PRKACA PRKAR2A PRKAR2B
+## [217] PRRC2B PSMD8 PTBP2
+## [220] PTGES2 PTGES2[0-513] PTGES2[512-2070]
+## [223] PUSL1 PVR QSOX2
+## [226] RAB10 RAB14 RAB18
+## [229] RAB1A RAB2A RAB5C
+## [232] RAB7A RAB8A RAE1
+## [235] RALA RAP1GDS1 RBM28
+## [238] RBM41 RBX1 REEP5
+## [241] REEP6 RETREG3 RHOA
+## [244] RIPK1 RNF41 RPL36
+## [247] RRP9 RTN4 SAAL1
+## [250] SBNO1 SCAP SCARB1
+## [253] SCARB1[0-2004] SCARB1[2003-2289] SCCPDH
+## [256] SELENOS[0-927] SELENOS[926-1137] SEPSECS
+## [259] SIGMAR1 SIL1 SIRT5
+## [262] SLC25A21 SLC27A2 SLC30A6
+## [265] SLC30A7 SLC30A9 SLC44A2
+## [268] SLC44A2[0-2820] SLC44A2[2819-3792] SLC9A3R1
+## [271] SLU7 SMOC1 SNIP1
+## [274] SPART SRP19 SRP54
+## [277] SRP72 STC2 STOM
+## [280] STOML2 SUN2 TAPT1
+## [283] TBK1 TBKBP1 TCF12
+## [286] THTPA TIMM10 TIMM10B
+## [289] TIMM29 TIMM8B TIMM9
+## [292] TLE1 TLE3 TLE5
+## [295] TM2D3 TMED5 TMEM97
+## [298] TOMM70 TOR1A TOR1AIP1
+## [301] TRIM59 TRMT1 TUBGCP2
+## [304] TUBGCP3 UBAP2 UBAP2L
+## [307] UBXN8 UGGT2 UPF1
+## [310] USP13 USP54 VPS11
+## [313] VPS39 WASHC4 WFS1
+## [316] YIF1A ZC3H18 ZC3H18[0-1101]
+## [319] ZC3H18[1100-3678] ZC3H7A ZDHHC5
+## [322] ZNF318 ZNF503 ZYG11B
+## [325] ATE1 FGFR1OP COL6A1
+## [328] COQ8B CYB5B DDX21
+## [331] ELOB ERO1B ETFA
+## [334] GNB1 GOLGA7 HSBP1
+## [337] INTS4 MOV10 MARC1
+## [340] PABPC1 PCSK6 PDE4DIP
+## [343] RDX REEP6-A REEP6-B
+## [346] SDF2 SELENOS TARS2
+## [349] TBCA TMEM39B TMPRSS2
+## [352] TMPRSS2 TYSND1
+## 352 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ... REEP6-B
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+Manual corrections:
+
+TMPRSS2 in bats
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnbats[dginnbats}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"TMPRSS2"}\hlstd{,]}
+\end{alltt}
+\begin{verbatim}
+## bats_File bats_Name Gene.name
+## 2810 TMPRSS2_bat_same_mafft_prank TMPRSS2 TMPRSS2
+## 2910 TMPRSS2_bat_select_cut_mafft_prank TMPRSS2 TMPRSS2
+## bats_GeneSize bats_NbSpecies bats_omegaM0Bpp
+## 2810 1174 12 0.140290584008726
+## 2910 574 12 0.129489038364869
+## bats_omegaM0codeml bats_BUSTED bats_BUSTED_p.value
+## 2810 0.145 N 0.9333
+## 2910 0.127 N 0.9358
+## bats_MEME_NbSites
+## 2810 12
+## 2910 19
+## bats_MEME_PSS
+## 2810 630, 644, 649, 688, 775, 888, 921, 1003, 1051, 1055, 1066, 1173
+## 2910 59, 73, 78, 108, 115, 117, 121, 133, 144, 241, 259, 288, 321, 403, 421, 451, 455, 466, 573
+## bats_BppM1M2 bats_BppM1M2_p.value bats_BppM1M2_NbSites
+## 2810 N 0.999999010422051 0
+## 2910 N 0.999999906049202 0
+## bats_BppM1M2_PSS bats_BppM7M8 bats_BppM7M8_p.value
+## 2810 na N 0.621882294670985
+## 2910 na N 0.334893426994811
+## bats_BppM7M8_NbSites bats_BppM7M8_PSS bats_codemlM1M2
+## 2810 0 na N
+## 2910 0 na N
+## bats_codemlM1M2_p.value bats_codemlM1M2_NbSites
+## 2810 1.0 0
+## 2910 1.0 0
+## bats_codemlM1M2_PSS bats_codemlM7M8 bats_codemlM7M8_p.value
+## 2810 na N 0.788991288016829
+## 2910 na N 0.4210515526274131
+## bats_codemlM7M8_NbSites bats_codemlM7M8_PSS
+## 2810 0 na
+## 2910 0 na
+## bats_Lucie.s.comments bats_Action.taken
+## 2810
+## 2910
+\end{verbatim}
+\begin{alltt}
+\hlcom{# keeping the uncut one}
+\hlcom{# renaming the other one TMPRSS2_cut}
+\hlstd{dginnbats[dginnbats}\hlopt{$}\hlstd{bats.File}\hlopt{==}\hlstr{"TMPRSS2_bat_select_cut_mafft_prank"}\hlstd{,}\hlstr{"Gene.name"}\hlstd{]}\hlkwb{<-}\hlstr{"TMPRSS2_cut"}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+RIPK1: ANcestral version kept, suppress it "RIPK1\_sequences\_filtered\_longestORFs\_mafft\_mincov\_prank"
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnT}\hlkwb{<-}\hlstd{dginnT[dginnT}\hlopt{$}\hlstd{File}\hlopt{!=}\hlstr{"RIPK1_sequences_filtered_longestORFs_mafft_mincov_prank"}\hlstd{,]}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+REEP6 eA et B
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{dginnbats[dginnbats}\hlopt{$}\hlstd{bats_File}\hlopt{==}\hlstr{"REEP6_sequences_filtered_longestORFs_D210gp1_prank"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{]}\hlkwb{<-}\hlstr{"REEP6_old"}
+\hlstd{dginnbats[dginnbats}\hlopt{$}\hlstd{bats_File}\hlopt{==}\hlstr{"REEP6_LA_bat_select_mafft_prank"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{]}\hlkwb{<-}\hlstr{"REEP6"}
+\hlstd{dginnbats[dginnbats}\hlopt{$}\hlstd{bats_File}\hlopt{==}\hlstr{"REEP6_LB_bat_select_mafft_prank"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{]}\hlkwb{<-}\hlstr{"REEP6_like"}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+GNG5
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnT}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{dginnT[dginnT}\hlopt{$}\hlstd{File}\hlopt{==}\hlstr{"GNG5_sequences_filtered_longestORFs_D189gp2_prank"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{]}\hlkwb{<-}\hlstr{"GNG5_like"}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{dim}\hlstd{(dginnbats)}
+\end{alltt}
+\begin{verbatim}
+## [1] 353 29
+\end{verbatim}
+\begin{alltt}
+\hlkwd{dim}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}
+## [1] 412 27
+\end{verbatim}
+\begin{alltt}
+\hlcom{# genes in common}
+\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name]}
+\end{alltt}
+\begin{verbatim}
+## [1] "AAR2" "AASS" "AATF" "ABCC1" "ACAD9"
+## [6] "ACADM" "ACE2" "ACSL3" "ADAM9" "ADAMTS1"
+## [11] "AGPS" "AKAP8" "AKAP8L" "AKAP9" "ALG11"
+## [16] "ALG5" "ALG8" "ANO6" "AP2A2" "AP2M1"
+## [21] "AP3B1" "ARF6" "ATE1" "ATP13A3" "ATP1B1"
+## [26] "ATP6AP1" "ATP6V1A" "BAG5" "BCKDK" "BRD2"
+## [31] "BRD4" "BZW2" "CCDC86" "CDK5RAP2" "CENPF"
+## [36] "CEP112" "CEP135" "CEP250" "CEP350" "CEP68"
+## [41] "CHMP2A" "CHPF" "CHPF2" "CISD3" "CIT"
+## [46] "CLCC1" "CLIP4" "CNTRL" "COL6A1" "COLGALT1"
+## [51] "COMT" "COQ8B" "CRTC3" "CSDE1" "CSNK2A2"
+## [56] "CSNK2B" "CUL2" "CWC27" "CYB5B" "DCAF7"
+## [61] "DCAKD" "DCTPP1" "DDX10" "DDX21" "DNAJC11"
+## [66] "DNAJC19" "DNMT1" "DPH5" "DPY19L1" "ECSIT"
+## [71] "EDEM3" "EIF4E2" "EIF4H" "ELOC" "EMC1"
+## [76] "ERC1" "ERGIC1" "ERLEC1" "ERMP1" "ERO1B"
+## [81] "ERP44" "ETFA" "EXOSC2" "EXOSC3" "EXOSC5"
+## [86] "EXOSC8" "F2RL1" "FAM162A" "FAM8A1" "FAM98A"
+## [91] "FAR2" "FASTKD5" "FBLN5" "FBN1" "FBN2"
+## [96] "FBXL12" "FKBP10" "FKBP15" "FKBP7" "FOXRED2"
+## [101] "FYCO1" "G3BP1" "G3BP2" "GCC1" "GCC2"
+## [106] "GDF15" "GFER" "GGCX" "GGH" "GHITM"
+## [111] "GIGYF2" "GLA" "GNB1" "GNG5" "GOLGA2"
+## [116] "GOLGA3" "GOLGA7" "GOLGB1" "GORASP1" "GPAA1"
+## [121] "GPX1" "GRIPAP1" "GRPEL1" "GTF2F2" "HDAC2"
+## [126] "HEATR3" "HECTD1" "HMOX1" "HOOK1" "HS2ST1"
+## [131] "HS6ST2" "HSBP1" "HYOU1" "IDE" "IL17RA"
+## [136] "IMPDH2" "INHBE" "INTS4" "ITGB1" "JAKMIP1"
+## [141] "LARP1" "LARP4B" "LARP7" "LMAN2" "LOX"
+## [146] "MAP7D1" "MARK1" "MARK2" "MARK3" "MAT2B"
+## [151] "MDN1" "MEPCE" "MIB1" "MIPOL1" "MOGS"
+## [156] "MOV10" "MPHOSPH10" "MRPS2" "MRPS25" "MRPS27"
+## [161] "MRPS5" "MARC1" "MTCH1" "MYCBP2" "NARS2"
+## [166] "NAT14" "NDFIP2" "NDUFAF1" "NDUFAF2" "NDUFB9"
+## [171] "NEK9" "NEU1" "NGDN" "NGLY1" "NIN"
+## [176] "NINL" "NLRX1" "NOL10" "NPC2" "NPTX1"
+## [181] "NSD2" "NUP210" "NUP214" "NUP54" "NUP58"
+## [186] "NUP62" "NUP88" "NUP98" "NUTF2" "OS9"
+## [191] "PABPC1" "PABPC4" "PCNT" "PCSK6" "PCSK5"
+## [196] "PDE4DIP" "PDZD11" "PIGO" "PIGS" "PITRM1"
+## [201] "PKP2" "PLAT" "PLD3" "PLEKHA5" "PLEKHF2"
+## [206] "PLOD2" "PMPCA" "PMPCB" "POFUT1" "KDELC1"
+## [211] "KDELC2" "POLA1" "POLA2" "POR" "PPIL3"
+## [216] "PPT1" "PRIM1" "PRIM2" "PRKACA" "PRKAR2A"
+## [221] "PRKAR2B" "PRRC2B" "PSMD8" "PTBP2" "PTGES2"
+## [226] "PUSL1" "PVR" "QSOX2" "RAB10" "RAB14"
+## [231] "RAB18" "RAB1A" "RAB2A" "RAB5C" "RAB7A"
+## [236] "RAB8A" "RAE1" "RALA" "RAP1GDS1" "RBM28"
+## [241] "RBM41" "RBX1" "RDX" "REEP5" "REEP6"
+## [246] "RETREG3" "RHOA" "RNF41" "RPL36" "RRP9"
+## [251] "RTN4" "SAAL1" "SBNO1" "SCAP" "SCARB1"
+## [256] "SCCPDH" "SDF2" "SEPSECS" "SIL1" "SIRT5"
+## [261] "SLC25A21" "SLC27A2" "SLC30A6" "SLC30A7" "SLC30A9"
+## [266] "SLC44A2" "SLC9A3R1" "SLU7" "SMOC1" "SNIP1"
+## [271] "SPART" "SRP19" "SRP54" "SRP72" "STC2"
+## [276] "STOM" "STOML2" "SUN2" "TAPT1" "TARS2"
+## [281] "TBCA" "TBK1" "TBKBP1" "TCF12" "THTPA"
+## [286] "TIMM10" "TIMM10B" "TIMM29" "TIMM8B" "TIMM9"
+## [291] "TLE1" "TLE3" "TM2D3" "TMED5" "TMEM39B"
+## [296] "TMEM97" "TMPRSS2" "TOMM70" "TOR1A" "TOR1AIP1"
+## [301] "TRIM59" "TRMT1" "TUBGCP2" "TUBGCP3" "TYSND1"
+## [306] "UBAP2" "UBAP2L" "UBXN8" "UGGT2" "UPF1"
+## [311] "USP54" "VPS11" "VPS39" "WASHC4" "WFS1"
+## [316] "YIF1A" "ZC3H18" "ZC3H7A" "ZDHHC5" "ZNF318"
+## [321] "ZNF503" "ZYG11B" "RIPK1"
+\end{verbatim}
+\begin{alltt}
+\hlkwd{length}\hlstd{(dginnT}\hlopt{$}\hlstd{Gene.name[dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name])}
+\end{alltt}
+\begin{verbatim}
+## [1] 323
+\end{verbatim}
+\begin{alltt}
+\hlcom{# genes only in primates}
+\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[(dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\end{alltt}
+\begin{verbatim}
+## [1] "ADAM9[0-3120]" "ADAM9[3119-3927]" "ATP5MGL"
+## [4] "BCS1L" "C1H1ORF50" "CEP135[0-3264]"
+## [7] "CEP135[3263-3678]" "CEP43" "COQ8A"
+## [10] "CSNK2A1" "CSNK2B[0-609]" "CSNK2B[608-2568]"
+## [13] "CYB5R3" "CYB5R1" "DDX21[0-717]"
+## [16] "DDX21[716-2538]" "DDX50" "DNAJC15"
+## [19] "DPH5[0-702]" "DPH5[701-1326]" "DPY19L2"
+## [22] "EXOSC3[0-1446]" "EXOSC3[1445-1980]" "FBN3"
+## [25] "GNB4" "GNB2" "GNB3"
+## [28] "GNG5_like" "GOLGA7[0-312]" "GOLGA7[311-549]"
+## [31] "GPX1[0-1218]" "GPX1[1217-2946]" "HDAC1"
+## [34] "HS6ST3" "IMPDH1" "ITGB1[0-2328]"
+## [37] "ITGB1[2327-2844]" "LMAN2L" "MRPS5[0-1569]"
+## [40] "MRPS5[1568-3783]" "MARC2" "MGRN1"
+## [43] "NDFIP2[0-768]" "NDFIP2[767-1314]" "NDUFAF2[0-258]"
+## [46] "NDUFAF2[257-744]" "NUP58[0-1824]" "NUP58[1823-2367]"
+## [49] "PABPC3" "POTPABPC1" "PABPC4L"
+## [52] "PABPC5" "PRIM2[0-1071]" "PRIM2[1070-1902]"
+## [55] "PRKACB" "PRKACG" "PTGES2[0-1587]"
+## [58] "PTGES2[1586-2202]" "RAB8B" "RAB13"
+## [61] "RAB18[0-855]" "RAB18[854-1815]" "RAB2B"
+## [64] "RAB5A" "RAB5B" "RAB15"
+## [67] "RALB" "EZR" "EZR[0-1458]"
+## [70] "EZR[1457-3771]" "MSN" "RHOB"
+## [73] "RHOC" "SLC44A2[0-2577]" "SLC44A2[2576-3657]"
+## [76] "SRP72[0-2604]" "SRP72[2603-3417]" "STOM[0-1047]"
+## [79] "STOM[1046-1800]" "STOML3" "TLE4"
+## [82] "TLE2" "TLE2[0-1302]" "TLE2[1301-3987]"
+## [85] "AES" "TOR1B" "WFS1[0-2346]"
+## [88] "WFS1[2345-3216]" "YIF1B"
+\end{verbatim}
+\begin{alltt}
+\hlkwd{length}\hlstd{(dginnT}\hlopt{$}\hlstd{Gene.name[(dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
+\end{alltt}
+\begin{verbatim}
+## [1] 89
+\end{verbatim}
+\begin{alltt}
+\hlcom{# genes only in bats}
+\hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name[(dginnbats}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\end{alltt}
+\begin{verbatim}
+## [1] "ADAM9[0-2769]" "ADAM9[2768-3030]" "ARL6IP6"
+## [4] "ATP5MG" "BCS1" "CUNH1ORF50"
+## [7] "CYB5BR3" "IDE[0-2343]" "IDE[2342-3240]"
+## [10] "IDE[3239-4911]" "MFGE8" "PTGES2[0-513]"
+## [13] "PTGES2[512-2070]" "REEP6_old" "SCARB1[0-2004]"
+## [16] "SCARB1[2003-2289]" "SELENOS[0-927]" "SELENOS[926-1137]"
+## [19] "SIGMAR1" "SLC44A2[0-2820]" "SLC44A2[2819-3792]"
+## [22] "TLE5" "USP13" "ZC3H18[0-1101]"
+## [25] "ZC3H18[1100-3678]" "FGFR1OP" "ELOB"
+## [28] "REEP6_like" "SELENOS"
+\end{verbatim}
+\begin{alltt}
+\hlkwd{length}\hlstd{(dginnbats}\hlopt{$}\hlstd{Gene.name[(dginnbats}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
+\end{alltt}
+\begin{verbatim}
+## [1] 29
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
\end{document}