<html><head><meta name="color-scheme" content="light dark"></head><body><pre style="word-wrap: break-word; white-space: pre-wrap;">\documentclass[11pt, oneside]{article}\usepackage[]{graphicx}\usepackage[]{color}
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\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
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\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\let\hlipl\hlkwb

\usepackage{framed}
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\definecolor{warningcolor}{rgb}{1, 0, 1}
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\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.
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\usepackage[utf8]{inputenc}
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%\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{&lt;-}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"}

\hlstd{tab}\hlkwb{&lt;-}\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{&lt;-}\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{&lt;-}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name[}\hlnum{158}\hlstd{]}\hlkwb{&lt;-}\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{&lt;-}\hlkwa{function}\hlstd{(}\hlkwc{method}\hlstd{=}\hlstr{"PamlM1M2"}\hlstd{)\{}

\hlstd{tmp}\hlkwb{&lt;-}\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{&lt;-}\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{&lt;-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}

\hlkwd{return}\hlstd{(tab)}
\hlstd{\}}

\hlstd{tab}\hlkwb{&lt;-}\hlkwd{add_col}\hlstd{(}\hlstr{"PamlM1M2"}\hlstd{)}
\hlstd{tab}\hlkwb{&lt;-}\hlkwd{add_col}\hlstd{(}\hlstr{"PamlM7M8"}\hlstd{)}
\hlstd{tab}\hlkwb{&lt;-}\hlkwd{add_col}\hlstd{(}\hlstr{"BppM1M2"}\hlstd{)}
\hlstd{tab}\hlkwb{&lt;-}\hlkwd{add_col}\hlstd{(}\hlstr{"BppM7M8"}\hlstd{)}


\hlcom{# Manip pour la colonne BUSTED}

\hlstd{tmp}\hlkwb{&lt;-}\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{&lt;-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"Omega_BUSTED"}\hlstd{,} \hlstr{"PosSel_BUSTED"}\hlstd{,} \hlstr{"PValue_BUSTED"}\hlstd{)}
\hlstd{tab}\hlkwb{&lt;-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}

\hlstd{tmp}\hlkwb{&lt;-}\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{&lt;-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"NbSites_MEME"}\hlstd{,} \hlstr{"PSS_MEME"}\hlstd{)}
\hlstd{tab}\hlkwb{&lt;-}\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{&lt;-}\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{&lt;-}\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{&lt;-}\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{&lt;-}\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{&lt;-}\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{&lt;-}\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{&lt;-}\hlstd{dginnbatsnew1}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{omegaM0codeml}\hlkwb{&lt;-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{omegaM0codeml}

\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM1M2}\hlkwb{&lt;-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM1M2}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM1M2_p.value}\hlkwb{&lt;-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM1M2_p.value}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM1M2_NbSites}\hlkwb{&lt;-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM1M2_NbSites}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM1M2_PSS}\hlkwb{&lt;-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM1M2_PSS}

\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM7M8}\hlkwb{&lt;-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM7M8}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM7M8_p.value}\hlkwb{&lt;-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM7M8_p.value}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM7M8_NbSites}\hlkwb{&lt;-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM7M8_NbSites}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM7M8_PSS}\hlkwb{&lt;-}\hlstd{dginnbatsnew2}\hlopt{$}\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{&lt;-}\hlkwd{as.vector}\hlstd{(dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,])}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_omegaM0Bpp`}\hlkwb{&lt;-}\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{$}\hlstd{`dginn-primate_BUSTED.p.value`}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{`dginn-primate_BppM1M2.p.value`}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{`dginn-primate_BppM7M8.p.value`}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{`dginn-primate_BppM7M8.PSS`}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.PSS`))}
\end{alltt}


{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.p.value`}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{`dginn-primate_codemlM1M2.PSS`}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.PSS`))}
\end{alltt}


{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8.p.value`}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{`dginn-primate_codemlM7M8.PSS`}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"GeneSize"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{GeneSize}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_NbSpecies"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{NbSpecies}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_omegaM0Bpp"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{omegaM0Bpp}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_omegaM0codeml"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{omegaM0codeml}

\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BUSTED"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BUSTED}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BUSTED.p.value"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BUSTED_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_MEME.NbSites"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{MEME_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_MEME.PSS"}\hlstd{]}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ripk1}\hlopt{$}\hlstd{MEME_PSS))}
\end{alltt}


{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM1M2}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.p.value"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM1M2_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.NbSites"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM1M2_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.PSS"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM1M2_PSS}

\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM7M8}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.p.value"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM7M8_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.NbSites"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM7M8_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.PSS"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM7M8_PSS}

\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM1M2}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.p.value"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM1M2_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.NbSites"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM1M2_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.PSS"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM1M2_PSS}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM7M8}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.p.value"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM7M8_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.NbSites"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM7M8_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.PSS"}\hlstd{]}\hlkwb{&lt;-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM7M8_PSS}

\hlcom{## 2. Remove it}
\hlstd{dginnbatsnew}\hlkwb{&lt;-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{!=}\hlstr{"RIPK1"}\hlstd{,]}


\hlcom{## suppress redundant lines}
\hlstd{dginnbats}\hlkwb{&lt;-}\hlstd{dginnbats[(dginnbats}\hlopt{$}\hlstd{Gene} \hlopt{%in%} \hlstd{dginnbatsnew}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlnum{FALSE}\hlstd{,]}
\hlkwd{names}\hlstd{(dginnbatsnew)}\hlkwb{&lt;-}\hlkwd{names}\hlstd{(dginnbats)}

\hlcom{##############"}
\hlstd{dginnbatsnew[,}\hlnum{4}\hlstd{]}\hlkwb{&lt;-}\hlkwd{as.numeric}\hlstd{(dginnbatsnew[,}\hlnum{4}\hlstd{])}
\hlstd{dginnbats[,}\hlnum{6}\hlstd{]}\hlkwb{&lt;-}\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{&lt;-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{8}\hlstd{])}
\hlstd{dginnbats[,}\hlnum{12}\hlstd{]}\hlkwb{&lt;-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{12}\hlstd{])}
\hlstd{dginnbats[,}\hlnum{13}\hlstd{]}\hlkwb{&lt;-}\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{&lt;-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{16}\hlstd{])}
\hlstd{dginnbats[,}\hlnum{17}\hlstd{]}\hlkwb{&lt;-}\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{&lt;-}\hlkwd{rbind}\hlstd{(dginnbats, dginnbatsnew)}

\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{&lt;-}\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{&lt;-}\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}

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