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<p>\documentclass[11pt, oneside]{article}\usepackage[]{graphicx}\usepackage[]{color}
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<p>\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
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\let\hlipl\hlkwb</p>
<p>\usepackage{framed}
\makeatletter
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\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>
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