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\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
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\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}}%
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\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{Data}

Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.


\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{"covid_comp/covid_comp_complete.txt"}\hlstd{),} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
\hlkwd{dim}\hlstd{(tab)}
\end{alltt}
\end{kframe}
\end{knitrout}



\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{"covid_comp/covid_comp_alldginn.txt"}\hlstd{),} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
\hlkwd{dim}\hlstd{(tab)}
\end{alltt}
\begin{verbatim}
## [1] 442  56
\end{verbatim}
\end{kframe}
\end{knitrout}

\section{Comparison of dataset}

\subsection{Data}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_BUSTED"}\hlstd{,} \hlstr{"bats_BppM1M2"}\hlstd{,} \hlstr{"bats_BppM7M8"}\hlstd{,}
    \hlstr{"bats_codemlM1M2"}\hlstd{,} \hlstr{"bats_codemlM7M8"}\hlstd{,} \hlstr{"dginn.primate_codemlM1M2"}\hlstd{,}
    \hlstr{"dginn.primate_codemlM7M8"}\hlstd{,} \hlstr{"dginn.primate_BppM1M2"}\hlstd{,}
    \hlstr{"dginn.primate_BppM7M8"}\hlstd{,} \hlstr{"dginn.primate_BUSTED"}\hlstd{)])}
\hlstd{col}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_BUSTED"}\hlstd{,} \hlstr{"bats_BppM1M2"}\hlstd{,} \hlstr{"bats_BppM7M8"}\hlstd{,}
    \hlstr{"bats_codemlM1M2"}\hlstd{,} \hlstr{"bats_codemlM7M8"}\hlstd{,} \hlstr{"dginn.primate_codemlM1M2"}\hlstd{,}
    \hlstr{"dginn.primate_codemlM7M8"}\hlstd{,} \hlstr{"dginn.primate_BppM1M2"}\hlstd{,}
    \hlstr{"dginn.primate_BppM7M8"}\hlstd{,} \hlstr{"dginn.primate_BUSTED"}\hlstd{)}
\hlkwd{dim}\hlstd{(tmp)}
\end{alltt}
\begin{verbatim}
## [1] 323  11
\end{verbatim}
\end{kframe}
\end{knitrout}

\subsection{Omega plot}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{x}\hlkwb{=}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp[tab}\hlopt{$}\hlstd{status}\hlopt{==}\hlstr{"shared"}\hlstd{]))}
\end{alltt}


{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{y}\hlkwb{=}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{bats_omegaM0Bpp[tab}\hlopt{$}\hlstd{status}\hlopt{==}\hlstr{"shared"}\hlstd{]))}
\end{alltt}


{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlkwd{names}\hlstd{(x)}\hlkwb{<-}\hlstd{tab}\hlopt{$}\hlstd{Gene.name[tab}\hlopt{$}\hlstd{status}\hlopt{==}\hlstr{"shared"}\hlstd{]}

\hlkwd{plot}\hlstd{(x,y,} \hlkwc{xlab}\hlstd{=}\hlstr{"bpp omega primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"bpp omega bats"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{)}
\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}
\hlkwd{abline}\hlstd{(}\hlkwd{lm}\hlstd{(y}\hlopt{~}\hlstd{x),} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}

\hlkwd{text}\hlstd{(x[x}\hlopt{>}\hlnum{0.5} \hlopt{&}\hlstd{y}\hlopt{<}\hlnum{0.4}\hlstd{], (y[x}\hlopt{>}\hlnum{0.5} \hlopt{&}\hlstd{y}\hlopt{<}\hlnum{0.4}\hlstd{]}\hlopt{+}\hlnum{0.01}\hlstd{),} \hlkwd{names}\hlstd{(x)[x}\hlopt{>}\hlnum{0.5} \hlopt{&}\hlstd{y}\hlopt{<}\hlnum{0.4}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.7}\hlstd{)}
\hlkwd{text}\hlstd{(x[x}\hlopt{<}\hlnum{0.45} \hlopt{&}\hlstd{y}\hlopt{>}\hlnum{0.45}\hlstd{], (y[x}\hlopt{<}\hlnum{0.45} \hlopt{&}\hlstd{y}\hlopt{>}\hlnum{0.45}\hlstd{]}\hlopt{+}\hlnum{0.01}\hlstd{),} \hlkwd{names}\hlstd{(x)[x}\hlopt{<}\hlnum{0.45} \hlopt{&}\hlstd{y}\hlopt{>}\hlnum{0.45}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.7}\hlstd{)}
\hlkwd{text}\hlstd{(x[x}\hlopt{>}\hlnum{0.45} \hlopt{&}\hlstd{y}\hlopt{>}\hlnum{0.4}\hlstd{], (y[x}\hlopt{>}\hlnum{0.45} \hlopt{&}\hlstd{y}\hlopt{>}\hlnum{0.4}\hlstd{]}\hlopt{+}\hlnum{0.01}\hlstd{),} \hlkwd{names}\hlstd{(x)[x}\hlopt{>}\hlnum{0.45} \hlopt{&}\hlstd{y}\hlopt{>}\hlnum{0.4}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.7}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/unnamed-chunk-3-1} 

\end{knitrout}

\subsection{Mondrian}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{library}\hlstd{(Mondrian)}

\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}

\hlstd{batstmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_codemlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tmp}\hlopt{$}\hlstd{bats_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{))}

\hlstd{primatetmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tmp}\hlopt{$}\hlstr{"dginn.primate_codemlM1M2"}\hlopt{==}\hlstr{"Y"}\hlstd{,}
  \hlstd{tmp}\hlopt{$}\hlstr{"dginn.primate_codemlM7M8"}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstr{"dginn.primate_BppM1M2"}\hlopt{==}\hlstr{"Y"}\hlstd{,}
  \hlstd{tmp}\hlopt{$}\hlstr{"dginn.primate_BppM7M8"}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstr{"dginn.primate_BUSTED"}\hlopt{==}\hlstr{"Y"}\hlstd{))}

\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn3}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(batstmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(primatetmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn4}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(batstmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(primatetmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}

\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{3}\hlstd{],} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN bats >3"}\hlstd{,} \hlstr{"DGINN primate >3"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianbats-1} 
\begin{kframe}\begin{alltt}
\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{4}\hlopt{:}\hlnum{5}\hlstd{],} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN bats >4"}\hlstd{,} \hlstr{"DGINN primate >4"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianbats-2} 

\end{knitrout}

\subsection{subsetR}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{library}\hlstd{(UpSetR)}

\hlkwd{upset}\hlstd{(monddata,} \hlkwc{nsets} \hlstd{=} \hlnum{4}\hlstd{,} \hlkwc{matrix.color} \hlstd{=} \hlstr{"#DC267F"}\hlstd{,}
\hlkwc{main.bar.color} \hlstd{=} \hlstr{"#648FFF"}\hlstd{,} \hlkwc{sets.bar.color} \hlstd{=} \hlstr{"#FE6100"}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/subsetbats-1} 
\begin{kframe}\begin{alltt}
\hlkwd{upset}\hlstd{(monddata[,}\hlnum{1}\hlopt{:}\hlnum{3}\hlstd{],} \hlkwc{nsets} \hlstd{=} \hlnum{2}\hlstd{,} \hlkwc{matrix.color} \hlstd{=} \hlstr{"#DC267F"}\hlstd{,}
\hlkwc{main.bar.color} \hlstd{=} \hlstr{"#648FFF"}\hlstd{,} \hlkwc{sets.bar.color} \hlstd{=} \hlstr{"#FE6100"}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/subsetbats-2} 
\begin{kframe}\begin{alltt}
\hlkwd{upset}\hlstd{(monddata[,}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{4}\hlstd{,}\hlnum{5}\hlstd{)],} \hlkwc{nsets} \hlstd{=} \hlnum{2}\hlstd{,} \hlkwc{matrix.color} \hlstd{=} \hlstr{"#DC267F"}\hlstd{,}
\hlkwc{main.bar.color} \hlstd{=} \hlstr{"#648FFF"}\hlstd{,} \hlkwc{sets.bar.color} \hlstd{=} \hlstr{"#FE6100"}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/subsetbats-3} 

\end{knitrout}

\section{Which are these genes?}

\subsection{Gene under positive selection in both bats and primates}

4 methods:

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 6           ACADM           1              1           1              1
## 7            ACE2           1              1           1              1
## 109           GGH           1              1           1              1
## 117        GOLGA7           1              1           1              1
## 134           IDE           1              1           1              1
## 139         ITGB1           1              1           1              1
## 146         LMAN2           1              1           1              1
## 212         POLA1           1              1           1              1
## 263       SLC27A2           1              1           1              1
## 301      TOR1AIP1           1              1           1              1
## 314         VPS39           1              1           1              1
\end{verbatim}
\end{kframe}
\end{knitrout}

3 methods:

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 6           ACADM           1              1           1              1
## 7            ACE2           1              1           1              1
## 9           ADAM9           1              1           0              0
## 34       CDK5RAP2           1              1           0              1
## 71          EDEM3           1              1           1              0
## 109           GGH           1              1           1              1
## 117        GOLGA7           1              1           1              1
## 134           IDE           1              1           1              1
## 139         ITGB1           1              1           1              1
## 146         LMAN2           1              1           1              1
## 157        MIPOL1           1              1           0              1
## 159         MOV10           1              1           0              0
## 212         POLA1           1              1           1              1
## 239      RAP1GDS1           1              1           1              0
## 257        SCCPDH           1              1           0              0
## 263       SLC27A2           1              1           1              1
## 301      TOR1AIP1           1              1           1              1
## 314         VPS39           1              1           1              1
\end{verbatim}
\end{kframe}
\end{knitrout}


\subsection{Gene under positive selection only in primates}

4 methods:

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 31           BRD4           0              1           0              1
## 34       CDK5RAP2           1              1           0              1
## 37         CEP135           0              1           0              1
## 40          CEP68           0              1           0              1
## 47          CLIP4           0              1           0              1
## 67          DNMT1           0              1           0              1
## 68           DPH5           0              1           0              1
## 75           EMC1           0              1           0              1
## 80          ERO1B           0              1           0              1
## 101         FYCO1           0              1           0              1
## 105          GCC2           0              1           0              1
## 110         GHITM           0              1           0              1
## 111        GIGYF2           0              1           0              1
## 112           GLA           0              1           0              1
## 127        HECTD1           0              1           0              1
## 143         LARP1           0              1           0              1
## 144        LARP4B           0              1           0              1
## 150         MARK1           0              1           0              1
## 157        MIPOL1           1              1           0              1
## 160     MPHOSPH10           0              1           0              1
## 166        MYCBP2           0              1           0              1
## 171       NDUFAF2           0              1           0              1
## 172        NDUFB9           0              1           0              1
## 187         NUP58           0              1           0              1
## 195          PCNT           0              1           0              1
## 218         PRIM2           0              1           0              1
## 220       PRKAR2A           0              1           0              1
## 227           PVR           0              1           0              1
## 245         REEP6           0              1           0              1
## 248         RIPK1           0              1           0              1
## 253         SAAL1           0              1           0              1
## 259       SEPSECS           0              1           0              1
## 261         SIRT5           0              1           0              1
## 262      SLC25A21           0              1           0              1
## 296       TMEM39B           0              1           0              1
## 298       TMPRSS2           0              1           0              1
## 304       TUBGCP2           0              1           0              1
## 307         UBAP2           0              1           0              1
## 310         UGGT2           0              1           0              1
## 321        ZNF318           0              1           0              1
\end{verbatim}
\end{kframe}
\end{knitrout}

3 methods:

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 19          AP2A2           0              1           0              0
## 23           ATE1           0              1           0              0
## 31           BRD4           0              1           0              1
## 32           BZW2           0              1           0              0
## 37         CEP135           0              1           0              1
## 40          CEP68           0              1           0              1
## 47          CLIP4           0              1           0              1
## 48          CNTRL           0              1           0              0
## 67          DNMT1           0              1           0              1
## 68           DPH5           0              1           0              1
## 72         EIF4E2           0              1           0              0
## 75           EMC1           0              1           0              1
## 80          ERO1B           0              1           0              1
## 83         EXOSC2           0              1           0              0
## 101         FYCO1           0              1           0              1
## 105          GCC2           0              1           0              1
## 110         GHITM           0              1           0              1
## 111        GIGYF2           0              1           0              1
## 112           GLA           0              1           0              1
## 118        GOLGB1           0              1           0              0
## 119       GORASP1           0              1           0              0
## 125         HDAC2           0              1           0              0
## 127        HECTD1           0              1           0              1
## 131        HS6ST2           0              1           0              0
## 143         LARP1           0              1           0              1
## 144        LARP4B           0              1           0              1
## 145         LARP7           0              1           0              0
## 150         MARK1           0              1           0              1
## 154          MDN1           0              1           0              0
## 160     MPHOSPH10           0              1           0              1
## 164         MRPS5           0              1           0              0
## 166        MYCBP2           0              1           0              1
## 168         NAT14           0              1           0              0
## 171       NDUFAF2           0              1           0              1
## 172        NDUFB9           0              1           0              1
## 176         NGLY1           0              1           0              0
## 181          NPC2           0              1           0              0
## 187         NUP58           0              1           0              1
## 195          PCNT           0              1           0              1
## 202        PITRM1           0              1           0              0
## 204          PLAT           0              1           0              0
## 208         PLOD2           0              1           0              0
## 210         PMPCB           0              1           0              0
## 214           POR           0              1           0              0
## 218         PRIM2           0              1           0              1
## 220       PRKAR2A           0              1           0              1
## 224         PTBP2           0              1           0              0
## 227           PVR           0              1           0              1
## 230         RAB14           0              1           0              0
## 232         RAB1A           0              1           0              0
## 233         RAB2A           0              1           0              0
## 242          RBX1           0              1           0              0
## 245         REEP6           0              1           0              1
## 248         RIPK1           0              1           0              1
## 250         RPL36           0              1           0              0
## 253         SAAL1           0              1           0              1
## 259       SEPSECS           0              1           0              1
## 261         SIRT5           0              1           0              1
## 262      SLC25A21           0              1           0              1
## 277          STOM           0              1           0              0
## 290        TIMM8B           0              1           0              0
## 296       TMEM39B           0              1           0              1
## 298       TMPRSS2           0              1           0              1
## 302        TRIM59           0              1           0              0
## 303         TRMT1           0              1           0              0
## 304       TUBGCP2           0              1           0              1
## 307         UBAP2           0              1           0              1
## 310         UGGT2           0              1           0              1
## 312         USP54           0              1           0              0
## 321        ZNF318           0              1           0              1
\end{verbatim}
\end{kframe}
\end{knitrout}


\subsection{Gene under positive selection only in bats}

4 methods:

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{0}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 14          AKAP9           1              0           1              0
## 26        ATP6AP1           1              0           1              0
## 44          CISD3           1              0           1              0
## 71          EDEM3           1              1           1              0
## 77         ERGIC1           1              0           1              0
## 136        IMPDH2           1              0           1              0
## 137         INHBE           1              0           1              0
## 231         RAB18           1              0           1              0
## 239      RAP1GDS1           1              1           1              0
## 267       SLC44A2           1              0           1              0
## 283          TBK1           1              0           1              0
\end{verbatim}
\end{kframe}
\end{knitrout}

3 methods:

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{0}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 5           ACAD9           1              0           0              0
## 11           AGPS           1              0           0              0
## 14          AKAP9           1              0           1              0
## 26        ATP6AP1           1              0           1              0
## 44          CISD3           1              0           1              0
## 49         COL6A1           1              0           0              0
## 77         ERGIC1           1              0           1              0
## 122       GRIPAP1           1              0           0              0
## 123        GRPEL1           1              0           0              0
## 136        IMPDH2           1              0           1              0
## 137         INHBE           1              0           1              0
## 151         MARK2           1              0           0              0
## 185        NUP214           1              0           0              0
## 217         PRIM1           1              0           0              0
## 226         PUSL1           1              0           0              0
## 231         RAB18           1              0           1              0
## 266       SLC30A9           1              0           0              0
## 267       SLC44A2           1              0           1              0
## 268      SLC9A3R1           1              0           0              0
## 283          TBK1           1              0           1              0
\end{verbatim}
\end{kframe}
\end{knitrout}

\subsection{Figure tableau}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tablo}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
\hlstd{tablo}\hlopt{$}\hlstd{nbats}\hlkwb{<-}\hlstd{batstmp}
\hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlkwb{<-}\hlstd{primatetmp}

\hlkwd{plot}\hlstd{(}\hlkwa{NULL}\hlstd{,} \hlkwc{xlim}\hlstd{=}\hlkwd{c}\hlstd{(}\hlopt{-}\hlnum{0.5}\hlstd{,}\hlnum{5.5}\hlstd{),} \hlkwc{ylim}\hlstd{=}\hlkwd{c}\hlstd{(}\hlopt{-}\hlnum{3}\hlstd{,}\hlnum{5.5}\hlstd{),} \hlkwc{xlab}\hlstd{=}\hlstr{"bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"primates"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"Genes supported by x,y methods in bats and primates"}\hlstd{,} \hlkwc{bty}\hlstd{=}\hlstr{"n"}\hlstd{,} \hlkwc{xaxt}\hlstd{=}\hlstr{"n"}\hlstd{,} \hlkwc{yaxt}\hlstd{=}\hlstr{"n"}\hlstd{)}

\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlopt{-}\hlnum{0.6}\hlstd{,} \hlnum{6}\hlstd{),} \hlkwc{y}\hlstd{=}\hlnum{0}\hlopt{:}\hlnum{5}\hlstd{,} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwc{y}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlopt{-}\hlnum{0.65}\hlstd{,} \hlnum{6}\hlstd{),} \hlkwc{x}\hlstd{=}\hlnum{0}\hlopt{:}\hlnum{5}\hlstd{,} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)}
\hlkwd{sapply}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlopt{-}\hlnum{0.5}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{by}\hlstd{=}\hlnum{1}\hlstd{),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)\{}
  \hlkwd{segments}\hlstd{(}\hlkwc{x0}\hlstd{=x,} \hlkwc{x1}\hlstd{=x,} \hlkwc{y0}\hlstd{=}\hlopt{-}\hlnum{0.5}\hlstd{,} \hlkwc{y1}\hlstd{=}\hlnum{5.5}\hlstd{)}
\hlstd{\})}
\end{alltt}
\begin{verbatim}
## [[1]]
## NULL
## 
## [[2]]
## NULL
## 
## [[3]]
## NULL
## 
## [[4]]
## NULL
## 
## [[5]]
## NULL
## 
## [[6]]
## NULL
## 
## [[7]]
## NULL
\end{verbatim}
\begin{alltt}
\hlkwd{sapply}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlopt{-}\hlnum{0.5}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{by}\hlstd{=}\hlnum{1}\hlstd{),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)\{}
  \hlkwd{segments}\hlstd{(}\hlkwc{x0}\hlstd{=}\hlopt{-}\hlnum{0.5}\hlstd{,} \hlkwc{x1}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{y0}\hlstd{=x,} \hlkwc{y1}\hlstd{=x)}
\hlstd{\})}
\end{alltt}
\begin{verbatim}
## [[1]]
## NULL
## 
## [[2]]
## NULL
## 
## [[3]]
## NULL
## 
## [[4]]
## NULL
## 
## [[5]]
## NULL
## 
## [[6]]
## NULL
## 
## [[7]]
## NULL
\end{verbatim}
\begin{alltt}
\hlkwa{for} \hlstd{(p} \hlkwa{in} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)\{}
  \hlkwa{for} \hlstd{(b} \hlkwa{in} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)\{}
    \hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlstd{b} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlstd{p]}
    \hlkwa{if}\hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{0} \hlopt{&} \hlkwd{length}\hlstd{(tmp)}\hlopt{<=}\hlnum{8}\hlstd{)\{}
      \hlkwd{text}\hlstd{(b,}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=(p}\hlopt{-}\hlnum{0.4}\hlstd{),} \hlkwc{to}\hlstd{=(p}\hlopt{+}\hlnum{0.4}\hlstd{),} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)), tmp,} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
    \hlstd{\}}\hlkwa{else if} \hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{8} \hlopt{&} \hlkwd{length}\hlstd{(tmp)}\hlopt{<=}\hlnum{16}\hlstd{)\{}
      \hlkwd{print}\hlstd{(}\hlkwd{c}\hlstd{(p, b))}
      \hlkwd{text}\hlstd{((b}\hlopt{-}\hlnum{0.3}\hlstd{),}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=(p}\hlopt{-}\hlnum{0.4}\hlstd{),} \hlkwc{to}\hlstd{=(p}\hlopt{+}\hlnum{0.4}\hlstd{),} \hlkwc{length.out} \hlstd{=} \hlnum{8}\hlstd{), tmp[}\hlnum{1}\hlopt{:}\hlnum{8}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
      \hlkwd{text}\hlstd{((b}\hlopt{+}\hlnum{0.3}\hlstd{),}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=(p}\hlopt{-}\hlnum{0.4}\hlstd{),} \hlkwc{to}\hlstd{=(p}\hlopt{+}\hlnum{0.4}\hlstd{),} \hlkwc{length.out} \hlstd{= (}\hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{8}\hlstd{)), tmp[}\hlnum{9}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
    \hlstd{\}}\hlkwa{else if} \hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{16}\hlstd{)\{}
      \hlkwd{text}\hlstd{(b,p,} \hlkwd{paste0}\hlstd{(}\hlkwd{length}\hlstd{(tmp),} \hlstr{" values"}\hlstd{))}
      \hlstd{\}}
  \hlstd{\}}
\hlstd{\}}
\end{alltt}
\begin{verbatim}
## [1] 1 2
## [1] 2 0
## [1] 2 1
## [1] 2 2
## [1] 3 0
## [1] 3 1
## [1] 4 0
## [1] 4 1
\end{verbatim}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{1}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{1.2}\hlstd{,} \hlstr{"p=1/n=0"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.1}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{18}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.3}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}

\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{1}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{1.7}\hlstd{,} \hlstr{"p=1/n=1"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.6}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{18}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{4.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.8}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}


\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{0}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{2.3}\hlstd{,} \hlstr{"p=0/n=0"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{17}\hlstd{),}\hlopt{-}\hlnum{2.1}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{17}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{17}\hlstd{),}\hlopt{-}\hlnum{2.3}\hlstd{, tmp[}\hlnum{18}\hlopt{:}\hlnum{34}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{34}\hlstd{),}\hlopt{-}\hlnum{2.5}\hlstd{, tmp[}\hlnum{35}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}


\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{2} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{0}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{2.9}\hlstd{,} \hlstr{"p=0/n=2"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{18}\hlstd{),}\hlopt{-}\hlnum{2.8}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{18}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{3.0}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/tablo-1} 

\end{knitrout}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{write.csv}\hlstd{(tablo[tablo}\hlopt{$}\hlstd{nbats}\hlopt{>=}\hlnum{3}\hlstd{,}\hlstr{"tmp$Gene.name"}\hlstd{],} \hlstr{"batssup3.csv"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)}

\hlkwd{write.csv}\hlstd{(tablo[tablo}\hlopt{$}\hlstd{nprimates}\hlopt{>=}\hlnum{3}\hlstd{,}\hlstr{"tmp$Gene.name"}\hlstd{],} \hlstr{"primatessup3.csv"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)}
\hlkwd{write.csv}\hlstd{(tablo,} \hlstr{"primatesVbats.csv"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}

Restreindre ce tableau aux gènes présent dans l'analyse de Krogan.

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlcom{# Reading the Krogan table}
\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}
\begin{alltt}
\hlcom{#Formating the column Gene.name and changing one wierd name}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name[tab}\hlopt{$}\hlstd{PreyGene}\hlopt{==}\hlstr{"MTARC1"}\hlstd{]}\hlkwb{<-}\hlstr{"MTARC1"}

\hlcom{#Adding ACE2 and TMPRSS2}
\hlstd{krogan}\hlkwb{<-}\hlkwd{c}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name,}  \hlstr{"ACE2"}\hlstd{,} \hlstr{"TMPRSS2"}\hlstd{)}

\hlcom{# The list}
\hlkwd{length}\hlstd{(krogan)}
\end{alltt}
\begin{verbatim}
## [1] 334
\end{verbatim}
\begin{alltt}
\hlstd{krogan}
\end{alltt}
\begin{verbatim}
##   [1] "PCNT"      "PVR"       "POLA1"     "FASTKD5"   "PRIM2"    
##   [6] "ITGB1"     "CNTRL"     "SIRT5"     "CEP250"    "MRPS5"    
##  [11] "CENPF"     "TRMT1"     "SAAL1"     "CEP68"     "NINL"     
##  [16] "AKAP9"     "NDUFAF2"   "GOLGB1"    "UGGT2"     "SEPSECS"  
##  [21] "ABCC1"     "CDK5RAP2"  "PDE4DIP"   "ACADM"     "PRRC2B"   
##  [26] "SLC25A21"  "PUSL1"     "NDUFB9"    "TOR1AIP1"  "MDN1"     
##  [31] "GCC2"      "ERLEC1"    "FYCO1"     "GHITM"     "GORASP1"  
##  [36] "USP54"     "ATE1"      "MRPS27"    "VPS39"     "CEP350"   
##  [41] "ALG11"     "MPHOSPH10" "SLC27A2"   "ALG8"      "BCS1L"    
##  [46] "STOM"      "NUP210"    "GOLGA2"    "EDEM3"     "DCTPP1"   
##  [51] "GIGYF2"    "UBAP2"     "DDX21"     "RAB18"     "MARK1"    
##  [56] "PRIM1"     "C19orf52"  "ZNF318"    "ALG5"      "EXOSC3"   
##  [61] "UBXN8"     "PABPC1"    "LMAN2"     "RIPK1"     "JAKMIP1"  
##  [66] "TARS2"     "NDUFAF1"   "PCSK6"     "ANO6"      "SNIP1"    
##  [71] "DNMT1"     "PRKAR2B"   "PLEKHA5"   "FKBP15"    "KDELC2"   
##  [76] "FBN1"      "NUP88"     "ATP13A3"   "TRIM59"    "NPC2"     
##  [81] "MEPCE"     "PLAT"      "EXOSC8"    "CEP135"    "GCC1"     
##  [86] "MIPOL1"    "YIF1A"     "AASS"      "GLA"       "FAM162A"  
##  [91] "FBXL12"    "EXOSC5"    "NGDN"      "ATP6AP1"   "LARP7"    
##  [96] "SIL1"      "NUP62"     "NDFIP2"    "COLGALT1"  "ECSIT"    
## [101] "EMC1"      "AP3B1"     "POLA2"     "CLIP4"     "SLU7"     
## [106] "CLCC1"     "ERO1LB"    "ATP5L"     "ERMP1"     "HS6ST2"   
## [111] "NUPL1"     "EIF4H"     "ZYG11B"    "EXOSC2"    "ADCK4"    
## [116] "WFS1"      "TAPT1"     "SPG20"     "NGLY1"     "FAR2"     
## [121] "CHMP2A"    "NLRX1"     "NUP214"    "PIGO"      "PITRM1"   
## [126] "ATP1B1"    "PPT1"      "HYOU1"     "TUBGCP2"   "KDELC1"   
## [131] "WHSC1"     "GDF15"     "NARS2"     "AKAP8"     "TBK1"     
## [136] "BRD4"      "GRIPAP1"   "PRKAR2A"   "MOGS"      "SCAP"     
## [141] "AATF"      "BRD2"      "FBN2"      "AKAP8L"    "OS9"      
## [146] "SIGMAR1"   "MTCH1"     "LARP4B"    "FAM134C"   "ARL6IP6"  
## [151] "RBM28"     "MRPS2"     "CEP112"    "LARP1"     "INHBE"    
## [156] "AGPS"      "MRPS25"    "MTARC1"    "F2RL1"     "MFGE8"    
## [161] "SLC9A3R1"  "CWC27"     "CYB5B"     "MAP7D1"    "IDE"      
## [166] "PMPCA"     "GGH"       "QSOX2"     "GNG5"      "PKP2"     
## [171] "PMPCB"     "RRP9"      "NIN"       "CUL2"      "ADAM9"    
## [176] "TMEM39B"   "RAB8A"     "CYB5R3"    "GPAA1"     "TM2D3"    
## [181] "COMT"      "SLC30A9"   "PLD3"      "CHPF"      "SRP19"    
## [186] "FKBP7"     "DDX10"     "ATP6V1A"   "AAR2"      "VIMP"     
## [191] "NAT14"     "MYCBP2"    "ERC1"      "DCAF7"     "FBLN5"    
## [196] "CSDE1"     "TCEB1"     "RAB14"     "BZW2"      "VPS11"    
## [201] "CIT"       "SLC30A6"   "DPY19L1"   "RTN4"      "AP2M1"    
## [206] "RNF41"     "TOR1A"     "PSMD8"     "SLC44A2"   "MOV10"    
## [211] "RAB10"     "NEU1"      "MIB1"      "TYSND1"    "USP13"    
## [216] "ZC3H7A"    "IMPDH2"    "DNAJC11"   "NEK9"      "PLEKHF2"  
## [221] "IL17RA"    "GNB1"      "GRPEL1"    "ARF6"      "FKBP10"   
## [226] "PABPC4"    "HMOX1"     "FOXRED2"   "NOL10"     "SRP72"    
## [231] "ZDHHC5"    "PTGES2"    "TMED5"     "HOOK1"     "POFUT1"   
## [236] "SUN2"      "ERP44"     "PRKACA"    "GOLGA3"    "ADAMTS1"  
## [241] "CSNK2B"    "THTPA"     "PIGS"      "RBM41"     "C1orf50"  
## [246] "TMEM97"    "RAB2A"     "STC2"      "SMOC1"     "FAM98A"   
## [251] "INTS4"     "RAB7A"     "HECTD1"    "STOML2"    "POR"      
## [256] "CSNK2A2"   "HS2ST1"    "DCAKD"     "SRP54"     "SDF2"     
## [261] "ZNF503"    "SBNO1"     "RAE1"      "TUBGCP3"   "UPF1"     
## [266] "ERGIC1"    "TLE1"      "TOMM70A"   "KIAA1033"  "DPH5"     
## [271] "UBAP2L"    "CHPF2"     "GFER"      "TIMM8B"    "RAB5C"    
## [276] "GOLGA7"    "TIMM10"    "HSBP1"     "BCKDK"     "ACSL3"    
## [281] "PDZD11"    "GGCX"      "RALA"      "LOX"       "TBKBP1"   
## [286] "CCDC86"    "NUP98"     "SCCPDH"    "SCARB1"    "CRTC3"    
## [291] "ETFA"      "FGFR1OP"   "SLC30A7"   "HEATR3"    "COL6A1"   
## [296] "RDX"       "G3BP1"     "TCF12"     "ZC3H18"    "G3BP2"    
## [301] "AP2A2"     "PLOD2"     "MARK2"     "TIMM9"     "TIMM10B"  
## [306] "RHOA"      "REEP5"     "REEP6"     "FAM8A1"    "PPIL3"    
## [311] "TLE3"      "AES"       "RAP1GDS1"  "HDAC2"     "GTF2F2"   
## [316] "NUP54"     "MAT2B"     "TCEB2"     "MARK3"     "PTBP2"    
## [321] "RPL36"     "TBCA"      "NUTF2"     "EIF4E2"    "GPX1"     
## [326] "RAB1A"     "DNAJC19"   "RBX1"      "CISD3"     "NPTX1"    
## [331] "BAG5"      "ACAD9"     "ACE2"      "TMPRSS2"
\end{verbatim}
\begin{alltt}
\hlcom{#In the table, I select line that match the krogan gene name liste}
\hlstd{tabloK}\hlkwb{<-}\hlstd{tablo[tablo}\hlopt{$}\hlstd{`tmp$Gene.name`} \hlopt{%in%} \hlstd{krogan,]}

\hlcom{# How many gene lost?}
\hlkwd{dim}\hlstd{(tablo)}
\end{alltt}
\begin{verbatim}
## [1] 323   3
\end{verbatim}
\begin{alltt}
\hlkwd{dim}\hlstd{(tabloK)}
\end{alltt}
\begin{verbatim}
## [1] 311   3
\end{verbatim}
\begin{alltt}
\hlcom{# Les gènes perdus (dans le tableau mais pas dans la liste de Krogan)}
\hlkwd{sort}\hlstd{(tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{`tmp$Gene.name`} \hlopt{%in%} \hlstd{krogan}\hlopt{==}\hlstd{F])}
\end{alltt}
\begin{verbatim}
##  [1] COQ8B   ELOC    ERO1B   MARC1   NSD2    NUP58   PCSK5   RETREG3
##  [9] SPART   TIMM29  TOMM70  WASHC4 
## 442 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ... ZYG11B
\end{verbatim}
\begin{alltt}
\hlcom{# Les gènes de Krogan non présent dans cette liste}
\hlkwd{sort}\hlstd{(krogan[krogan} \hlopt{%in%} \hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`}\hlopt{==}\hlstd{F])}
\end{alltt}
\begin{verbatim}
##  [1] "ADCK4"    "AES"      "ARL6IP6"  "ATP5L"    "BCS1L"    "C19orf52"
##  [7] "C1orf50"  "CYB5R3"   "ERO1LB"   "FAM134C"  "FGFR1OP"  "KIAA1033"
## [13] "MFGE8"    "MTARC1"   "NUPL1"    "SIGMAR1"  "SPG20"    "TCEB1"   
## [19] "TCEB2"    "TOMM70A"  "USP13"    "VIMP"     "WHSC1"
\end{verbatim}
\begin{alltt}
\hlkwd{write.csv}\hlstd{(tabloK,} \hlstr{"primatesVbats_onlykrogan.csv"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}


\end{document}




