diff --git a/covid_comp_script0_table.Rnw b/covid_comp_script0_table.Rnw
new file mode 100644
index 0000000000000000000000000000000000000000..7243ad4eb56975729ac69194a134b2bb9983bc29
--- /dev/null
+++ b/covid_comp_script0_table.Rnw
@@ -0,0 +1,249 @@
+\documentclass[11pt, oneside]{article} % 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
+%\usepackage{amssymb}
+
+\usepackage[utf8]{inputenc}
+%\usepackage[cyr]{aeguill}
+%\usepackage[francais]{babel}
+%\usepackage{hyperref}
+
+
+\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
+
+\begin{document}
+\maketitle
+
+\tableofcontents
+
+\newpage
+
+\section{Files manipulations}
+
+\subsection{Read Janet Young's table}
+
+<<>>=
+workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"
+
+tab<-read.delim(paste0(workdir,
+ "data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"),
+ fill=T, h=T, dec=",")
+dim(tab)
+@
+
+\subsection{Read DGINN Young table}
+
+<<>>=
+dginnY<-read.delim(paste0(workdir,
+ "data/summary_primate_young.res"),
+ fill=T, h=T)
+
+dim(dginnY)
+@
+
+\subsection{Joining Young and DGINN Young table}
+
+<<>>=
+# correct gene names (MARC1)
+val_remp=as.character(unique(dginnY$Gene)[(unique(dginnY$Gene) %in%
+ tab$Gene.name)==F])
+tab$Gene.name<-as.character(tab$Gene.name)
+tab$Gene.name[158]<-val_remp
+sum(unique(dginnY$Gene) %in% unique(tab$Gene.name))
+@
+
+<<>>=
+
+add_col<-function(method="PamlM1M2"){
+
+tmp<-dginnY[dginnY$Method==method,
+ c("Gene", "Omega", "PosSel", "PValue", "NbSites", "PSS")]
+
+names(tmp)<-c("Gene.name", paste0("Omega_", method),
+ paste0("PosSel_", method), paste0("PValue_", method),
+ paste0("NbSites_", method), paste0("PSS_", method))
+
+tab<-merge(tab, tmp, by="Gene.name")
+
+return(tab)
+}
+
+tab<-add_col("PamlM1M2")
+tab<-add_col("PamlM7M8")
+tab<-add_col("BppM1M2")
+tab<-add_col("BppM7M8")
+
+
+# Manip pour la colonne BUSTED
+
+tmp<-dginnY[dginnY$Method=="BUSTED",c("Gene", "Omega", "PosSel", "PValue")]
+names(tmp)<-c("Gene.name", "Omega_BUSTED", "PosSel_BUSTED", "PValue_BUSTED")
+tab<-merge(tab, tmp, by="Gene.name")
+
+tmp<-dginnY[dginnY$Method=="MEME",c("Gene", "NbSites", "PSS")]
+names(tmp)<-c("Gene.name", "NbSites_MEME", "PSS_MEME")
+tab<-merge(tab, tmp, by="Gene.name")
+
+@
+
+
+\subsection{Read DGINN Table}
+
+<<>>=
+dginnT<-read.delim(paste0(workdir,
+ "data/DGINN_202005281649summary_cleaned.csv"),
+ fill=T, h=T, sep=",")
+
+dim(dginnT)
+
+names(dginnT)
+
+# Number of genes in dginn-primate output not present in the original table
+dginnT[(dginnT$Gene %in% tab$Gene.name)==F,"Gene"]
+# This includes paralogs, recombinations found by DGINN and additionnal genes
+# included on purpose
+
+# Number of genes from the original list not present in DGINN output
+tab[(tab$Gene.name %in% dginnT$Gene)==F,"Gene.name"]
+
+
+names(dginnT)<-c("File", "Name", "Gene.name", "GeneSize",
+ "dginn-primate_NbSpecies", "dginn-primate_omegaM0Bpp",
+ "dginn-primate_omegaM0codeml", "dginn-primate_BUSTED",
+ "dginn-primate_BUSTED.p.value", "dginn-primate_MEME.NbSites",
+ "dginn-primate_MEME.PSS", "dginn-primate_BppM1M2",
+ "dginn-primate_BppM1M2.p.value", "dginn-primate_BppM1M2.NbSites",
+ "dginn-primate_BppM1M2.PSS", "dginn-primate_BppM7M8",
+ "dginn-primate_BppM7M8.p.value", "dginn-primate_BppM7M8.NbSites",
+ "dginn-primate_BppM7M8.PSS", "dginn-primate_codemlM1M2",
+ "dginn-primate_codemlM1M2.p.value", "dginn-primate_codemlM1M2.NbSites",
+ "dginn-primate_codemlM1M2.PSS", "dginn-primate_codemlM7M8",
+ "dginn-primate_codemlM7M8.p.value", "dginn-primate_codemlM7M8.NbSites",
+ "dginn-primate_codemlM7M8.PSS")
+@
+
+\subsection{Join Table and DGINN table}
+
+<<>>=
+tab<-merge(tab,dginnT, by="Gene.name", all.x=T)
+@
+
+\subsection{Add DGINN results on bat dataset}
+
+DGINN results from different analysis.
+
+<<>>=
+# original table
+dginnbats<-read.delim(paste0(workdir,
+ "data/DGINN_202005281339summary_cleaned.tab"),
+ fill=T, h=T)
+
+# rerun on corrected alignment
+dginnbatsnew1<-read.delim(paste0(workdir,
+ "data/DGINN_202011262248_summary.tab"),
+ fill=T, h=T)
+dginnbatsnew2<-read.delim(paste0(workdir,
+ "data/DGINN_202012192053_summary.tab"),
+ fill=T, h=T)
+
+# colomne choice, BUSTED and Bppml form first file, codeml from the other one
+
+dginnbatsnew<-dginnbatsnew1
+dginnbatsnew$omegaM0codeml<-dginnbatsnew2$omegaM0codeml
+
+dginnbatsnew$codemlM1M2<-dginnbatsnew2$codemlM1M2
+dginnbatsnew$codemlM1M2_p.value<-dginnbatsnew2$codemlM1M2_p.value
+dginnbatsnew$codemlM1M2_NbSites<-dginnbatsnew2$codemlM1M2_NbSites
+dginnbatsnew$codemlM1M2_PSS<-dginnbatsnew2$codemlM1M2_PSS
+
+dginnbatsnew$codemlM7M8<-dginnbatsnew2$codemlM7M8
+dginnbatsnew$codemlM7M8_p.value<-dginnbatsnew2$codemlM7M8_p.value
+dginnbatsnew$codemlM7M8_NbSites<-dginnbatsnew2$codemlM7M8_NbSites
+dginnbatsnew$codemlM7M8_PSS<-dginnbatsnew2$codemlM7M8_PSS
+
+####
+## RIPK1 is actually a primat results
+## 1. Take it and put it at the right place
+ripk1<-as.vector(dginnbatsnew[dginnbatsnew$Gene=="RIPK1",])
+tab$`dginn-primate_omegaM0Bpp`<-as.numeric(as.character(tab$`dginn-primate_omegaM0Bpp`))
+tab$`dginn-primate_BUSTED.p.value`<-as.numeric(as.character(tab$`dginn-primate_BUSTED.p.value`))
+tab$`dginn-primate_BppM1M2.p.value`<-as.numeric(as.character(tab$`dginn-primate_BppM1M2.p.value`))
+tab$`dginn-primate_BppM7M8.p.value`<-as.numeric(as.character(tab$`dginn-primate_BppM7M8.p.value`))
+tab$`dginn-primate_BppM7M8.PSS`<-as.numeric(as.character(tab$`dginn-primate_BppM7M8.PSS`))
+tab$`dginn-primate_codemlM1M2.p.value`<-as.numeric(as.character(tab$`dginn-primate_codemlM1M2.p.value`))
+tab$`dginn-primate_codemlM1M2.PSS`<-as.numeric(as.character(tab$`dginn-primate_codemlM1M2.PSS`))
+tab$`dginn-primate_codemlM7M8.p.value`<-as.numeric(as.character(tab$`dginn-primate_codemlM7M8.p.value`))
+tab$`dginn-primate_codemlM7M8.PSS`<-as.numeric(as.character(tab$`dginn-primate_codemlM7M8.PSS`))
+
+tab[tab$Gene.name=="RIPK1","GeneSize"]<-ripk1$GeneSize
+tab[tab$Gene.name=="RIPK1","dginn-primate_NbSpecies"]<-ripk1$NbSpecies
+tab[tab$Gene.name=="RIPK1","dginn-primate_omegaM0Bpp"]<-ripk1$omegaM0Bpp
+tab[tab$Gene.name=="RIPK1","dginn-primate_omegaM0codeml"]<-ripk1$omegaM0codeml
+
+tab[tab$Gene.name=="RIPK1","dginn-primate_BUSTED"]<-ripk1$BUSTED
+tab[tab$Gene.name=="RIPK1","dginn-primate_BUSTED.p.value"]<-ripk1$BUSTED_p.value
+tab[tab$Gene.name=="RIPK1","dginn-primate_MEME.NbSites"]<-ripk1$MEME_NbSites
+tab[tab$Gene.name=="RIPK1","dginn-primate_MEME.PSS"]<-as.numeric(as.character(ripk1$MEME_PSS))
+
+tab[tab$Gene.name=="RIPK1","dginn-primate_BppM1M2"]<-ripk1$BppM1M2
+tab[tab$Gene.name=="RIPK1","dginn-primate_BppM1M2.p.value"]<-ripk1$BppM1M2_p.value
+tab[tab$Gene.name=="RIPK1","dginn-primate_BppM1M2.NbSites"]<-ripk1$BppM1M2_NbSites
+tab[tab$Gene.name=="RIPK1","dginn-primate_BppM1M2.PSS"]<-ripk1$BppM1M2_PSS
+
+tab[tab$Gene.name=="RIPK1","dginn-primate_BppM7M8"]<-ripk1$BppM7M8
+tab[tab$Gene.name=="RIPK1","dginn-primate_BppM7M8.p.value"]<-ripk1$BppM7M8_p.value
+tab[tab$Gene.name=="RIPK1","dginn-primate_BppM7M8.NbSites"]<-ripk1$BppM7M8_NbSites
+tab[tab$Gene.name=="RIPK1","dginn-primate_BppM7M8.PSS"]<-ripk1$BppM7M8_PSS
+
+tab[tab$Gene.name=="RIPK1","dginn-primate_codemlM1M2"]<-ripk1$codemlM1M2
+tab[tab$Gene.name=="RIPK1","dginn-primate_codemlM1M2.p.value"]<-ripk1$codemlM1M2_p.value
+tab[tab$Gene.name=="RIPK1","dginn-primate_codemlM1M2.NbSites"]<-ripk1$codemlM1M2_NbSites
+tab[tab$Gene.name=="RIPK1","dginn-primate_codemlM1M2.PSS"]<-ripk1$codemlM1M2_PSS
+tab[tab$Gene.name=="RIPK1","dginn-primate_codemlM7M8"]<-ripk1$codemlM7M8
+tab[tab$Gene.name=="RIPK1","dginn-primate_codemlM7M8.p.value"]<-ripk1$codemlM7M8_p.value
+tab[tab$Gene.name=="RIPK1","dginn-primate_codemlM7M8.NbSites"]<-ripk1$codemlM7M8_NbSites
+tab[tab$Gene.name=="RIPK1","dginn-primate_codemlM7M8.PSS"]<-ripk1$codemlM7M8_PSS
+
+## 2. Remove it
+dginnbatsnew<-dginnbatsnew[dginnbatsnew$Gene!="RIPK1",]
+
+
+## suppress redundant lines
+dginnbats<-dginnbats[(dginnbats$Gene %in% dginnbatsnew$Gene)==FALSE,]
+names(dginnbatsnew)<-names(dginnbats)
+
+##############"
+dginnbatsnew[,4]<-as.numeric(dginnbatsnew[,4])
+dginnbats[,6]<-as.numeric(as.character(dginnbats[,6]))
+dginnbats[,8]<-as.character(dginnbats[,8])
+dginnbats[,12]<-as.character(dginnbats[,12])
+dginnbats[,13]<-as.numeric(as.character(dginnbats[,13]))
+dginnbats[,16]<-as.character(dginnbats[,16])
+dginnbats[,17]<-as.numeric(as.character(dginnbats[,17]))
+
+## replace by new data
+dginnbats<-rbind(dginnbats, dginnbatsnew)
+
+names(dginnbats)<-c("File", "bats_Name", "cooper.batsGene", paste0("bats_",
+ names(dginnbats)[-(1:3)]))
+names(dginnbats)
+
+tab<-merge(tab,dginnbats, by="cooper.batsGene", all.x=T)
+
+@
+
+\subsection{Write the new table}
+
+<<>>=
+
+write.table(tab, "covid_comp_complete.txt", row.names=FALSE, quote=FALSE, sep="\t")
+@
+
+\end{document}
+
diff --git a/covid_comp_script0_table.pdf b/covid_comp_script0_table.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..669dd5b72c62078bbb831a30e6085797bff4df95
Binary files /dev/null and b/covid_comp_script0_table.pdf differ
diff --git a/covid_comp_script0_table.tex b/covid_comp_script0_table.tex
new file mode 100644
index 0000000000000000000000000000000000000000..c8b1af626e8cf56061f18834acff7cdbb2a492db
--- /dev/null
+++ b/covid_comp_script0_table.tex
@@ -0,0 +1,434 @@
+\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
+
+\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
+
+\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
+
+\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
+
+\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
+%\usepackage{amssymb}
+
+\usepackage[utf8]{inputenc}
+%\usepackage[cyr]{aeguill}
+%\usepackage[francais]{babel}
+%\usepackage{hyperref}
+
+
+\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
+
+\tableofcontents
+
+\newpage
+
+\section{Files manipulations}
+
+\subsection{Read Janet Young's table}
+
+\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/"}
+
+\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}
+## [1] 332 84
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+\subsection{Read DGINN Young table}
+
+\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)}
+
+\hlkwd{dim}\hlstd{(dginnY)}
+\end{alltt}
+\begin{verbatim}
+## [1] 1992 7
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+\subsection{Joining Young and DGINN Young table}
+
+\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{$}\hlstd{Gene.name))}
+\end{alltt}
+\begin{verbatim}
+## [1] 332
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{add_col}\hlkwb{<-}\hlkwa{function}\hlstd{(}\hlkwc{method}\hlstd{=}\hlstr{"PamlM1M2"}\hlstd{)\{}
+
+\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\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{)]}
+
+\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{"Omega_"}\hlstd{, method),}
+ \hlkwd{paste0}\hlstd{(}\hlstr{"PosSel_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{"PValue_"}\hlstd{, method),}
+ \hlkwd{paste0}\hlstd{(}\hlstr{"NbSites_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{"PSS_"}\hlstd{, method))}
+
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
+
+\hlkwd{return}\hlstd{(tab)}
+\hlstd{\}}
+
+\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{)}
+
+
+\hlcom{# Manip pour la colonne BUSTED}
+
+\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{"BUSTED"}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"Omega"}\hlstd{,} \hlstr{"PosSel"}\hlstd{,} \hlstr{"PValue"}\hlstd{)]}
+\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"Omega_BUSTED"}\hlstd{,} \hlstr{"PosSel_BUSTED"}\hlstd{,} \hlstr{"PValue_BUSTED"}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
+
+\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\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}
+
+
+\subsection{Read DGINN Table}
+
+\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" "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"
+\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]
+## [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
+\end{verbatim}
+\begin{alltt}
+\hlcom{# This includes paralogs, recombinations found by DGINN and additionnal genes }
+\hlcom{# included on purpose}
+
+\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}
+## [1] "ADCK4" "ARL6IP6" "ATP5L" "C19orf52" "C1orf50" "ERO1LB" "FAM134C" "FGFR1OP" "KIAA1033" "MFGE8" "NUPL1"
+## [12] "SIGMAR1" "SPG20" "TCEB1" "TCEB2" "TOMM70A" "USP13" "VIMP" "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{,}
+ \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{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)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\subsection{Add DGINN results on bat dataset}
+
+DGINN results from different analysis.
+
+\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)}
+
+\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)}
+
+\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}
+
+\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}
+
+\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}
+
+\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{`dginn-primate_omegaM0Bpp`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_omegaM0Bpp`))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BUSTED.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BUSTED.p.value`))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BppM1M2.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BppM1M2.p.value`))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.p.value`))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.PSS`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.PSS`))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.p.value`))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.PSS`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.PSS`))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8.p.value`))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8.PSS`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8.PSS`))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab[tab}\hlopt{$}\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{$}\hlstd{omegaM0codeml}
+
+\hlstd{tab[tab}\hlopt{$}\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{$}\hlstd{MEME_PSS))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tab[tab}\hlopt{$}\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{$}\hlstd{BppM1M2_PSS}
+
+\hlstd{tab[tab}\hlopt{$}\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{$}\hlstd{BppM7M8_PSS}
+
+\hlstd{tab[tab}\hlopt{$}\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{$}\hlstd{codemlM7M8_PSS}
+
+\hlcom{## 2. Remove it}
+\hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\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{##############"}
+\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}
+
+
+{\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}
+
+
+{\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}
+
+
+{\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)}
+
+\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"bats_Name"}\hlstd{,} \hlstr{"cooper.batsGene"}\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] "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"
+\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}
+
+\subsection{Write the new table}
+
+\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}
+
+\end{document}
+