<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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\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\let\hlipl\hlkwb

\usepackage{framed}
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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.
%\geometry{letterpaper}                   		% ... or a4paper or a5paper or ... 
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\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{&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{"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{&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{"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{&lt;-}\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{&lt;-}\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{&lt;-}\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{&gt;}\hlnum{0.5} \hlopt{&amp;}\hlstd{y}\hlopt{&lt;}\hlnum{0.4}\hlstd{], (y[x}\hlopt{&gt;}\hlnum{0.5} \hlopt{&amp;}\hlstd{y}\hlopt{&lt;}\hlnum{0.4}\hlstd{]}\hlopt{+}\hlnum{0.01}\hlstd{),} \hlkwd{names}\hlstd{(x)[x}\hlopt{&gt;}\hlnum{0.5} \hlopt{&amp;}\hlstd{y}\hlopt{&lt;}\hlnum{0.4}\hlstd{])}
\hlkwd{text}\hlstd{(x[x}\hlopt{&lt;}\hlnum{0.45} \hlopt{&amp;}\hlstd{y}\hlopt{&gt;}\hlnum{0.45}\hlstd{], (y[x}\hlopt{&lt;}\hlnum{0.45} \hlopt{&amp;}\hlstd{y}\hlopt{&gt;}\hlnum{0.45}\hlstd{]}\hlopt{+}\hlnum{0.01}\hlstd{),} \hlkwd{names}\hlstd{(x)[x}\hlopt{&lt;}\hlnum{0.45} \hlopt{&amp;}\hlstd{y}\hlopt{&gt;}\hlnum{0.45}\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{&lt;-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}

\hlstd{batstmp}\hlkwb{&lt;-}\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{&lt;-}\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{$}\hlstd{bats_dginn3}\hlkwb{&lt;-}\hlkwd{ifelse}\hlstd{(batstmp}\hlopt{&gt;=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlkwb{&lt;-}\hlkwd{ifelse}\hlstd{(primatetmp}\hlopt{&gt;=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn4}\hlkwb{&lt;-}\hlkwd{ifelse}\hlstd{(batstmp}\hlopt{&gt;=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlkwb{&lt;-}\hlkwd{ifelse}\hlstd{(primatetmp}\hlopt{&gt;=}\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 &gt;3"}\hlstd{,} \hlstr{"DGINN primate &gt;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 &gt;4"}\hlstd{,} \hlstr{"DGINN primate &gt;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{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{1} \hlopt{&amp;} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
## 6           ACADM           1              1           1
## 7            ACE2           1              1           1
## 109           GGH           1              1           1
## 117        GOLGA7           1              1           1
## 134           IDE           1              1           1
## 139         ITGB1           1              1           1
## 146         LMAN2           1              1           1
## 212         POLA1           1              1           1
## 263       SLC27A2           1              1           1
## 301      TOR1AIP1           1              1           1
## 314         VPS39           1              1           1
##     primate_dginn4
## 6                1
## 7                1
## 109              1
## 117              1
## 134              1
## 139              1
## 146              1
## 212              1
## 263              1
## 301              1
## 314              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{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{1} \hlopt{&amp;} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
## 6           ACADM           1              1           1
## 7            ACE2           1              1           1
## 9           ADAM9           1              1           0
## 34       CDK5RAP2           1              1           0
## 71          EDEM3           1              1           1
## 109           GGH           1              1           1
## 117        GOLGA7           1              1           1
## 134           IDE           1              1           1
## 139         ITGB1           1              1           1
## 146         LMAN2           1              1           1
## 157        MIPOL1           1              1           0
## 159         MOV10           1              1           0
## 212         POLA1           1              1           1
## 239      RAP1GDS1           1              1           1
## 257        SCCPDH           1              1           0
## 263       SLC27A2           1              1           1
## 301      TOR1AIP1           1              1           1
## 314         VPS39           1              1           1
##     primate_dginn4
## 6                1
## 7                1
## 9                0
## 34               1
## 71               0
## 109              1
## 117              1
## 134              1
## 139              1
## 146              1
## 157              1
## 159              0
## 212              1
## 239              0
## 257              0
## 263              1
## 301              1
## 314              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{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{0} \hlopt{&amp;} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
## 31           BRD4           0              1           0
## 34       CDK5RAP2           1              1           0
## 37         CEP135           0              1           0
## 40          CEP68           0              1           0
## 47          CLIP4           0              1           0
## 67          DNMT1           0              1           0
## 68           DPH5           0              1           0
## 75           EMC1           0              1           0
## 80          ERO1B           0              1           0
## 101         FYCO1           0              1           0
## 105          GCC2           0              1           0
## 110         GHITM           0              1           0
## 111        GIGYF2           0              1           0
## 112           GLA           0              1           0
## 127        HECTD1           0              1           0
## 143         LARP1           0              1           0
## 144        LARP4B           0              1           0
## 150         MARK1           0              1           0
## 157        MIPOL1           1              1           0
## 160     MPHOSPH10           0              1           0
## 166        MYCBP2           0              1           0
## 171       NDUFAF2           0              1           0
## 172        NDUFB9           0              1           0
## 187         NUP58           0              1           0
## 195          PCNT           0              1           0
## 218         PRIM2           0              1           0
## 220       PRKAR2A           0              1           0
## 227           PVR           0              1           0
## 245         REEP6           0              1           0
## 248         RIPK1           0              1           0
## 253         SAAL1           0              1           0
## 259       SEPSECS           0              1           0
## 261         SIRT5           0              1           0
## 262      SLC25A21           0              1           0
## 296       TMEM39B           0              1           0
## 298       TMPRSS2           0              1           0
## 304       TUBGCP2           0              1           0
## 307         UBAP2           0              1           0
## 310         UGGT2           0              1           0
## 321        ZNF318           0              1           0
##     primate_dginn4
## 31               1
## 34               1
## 37               1
## 40               1
## 47               1
## 67               1
## 68               1
## 75               1
## 80               1
## 101              1
## 105              1
## 110              1
## 111              1
## 112              1
## 127              1
## 143              1
## 144              1
## 150              1
## 157              1
## 160              1
## 166              1
## 171              1
## 172              1
## 187              1
## 195              1
## 218              1
## 220              1
## 227              1
## 245              1
## 248              1
## 253              1
## 259              1
## 261              1
## 262              1
## 296              1
## 298              1
## 304              1
## 307              1
## 310              1
## 321              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{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{0} \hlopt{&amp;} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
## 19          AP2A2           0              1           0
## 23           ATE1           0              1           0
## 31           BRD4           0              1           0
## 32           BZW2           0              1           0
## 37         CEP135           0              1           0
## 40          CEP68           0              1           0
## 47          CLIP4           0              1           0
## 48          CNTRL           0              1           0
## 67          DNMT1           0              1           0
## 68           DPH5           0              1           0
## 72         EIF4E2           0              1           0
## 75           EMC1           0              1           0
## 80          ERO1B           0              1           0
## 83         EXOSC2           0              1           0
## 101         FYCO1           0              1           0
## 105          GCC2           0              1           0
## 110         GHITM           0              1           0
## 111        GIGYF2           0              1           0
## 112           GLA           0              1           0
## 118        GOLGB1           0              1           0
## 119       GORASP1           0              1           0
## 125         HDAC2           0              1           0
## 127        HECTD1           0              1           0
## 131        HS6ST2           0              1           0
## 143         LARP1           0              1           0
## 144        LARP4B           0              1           0
## 145         LARP7           0              1           0
## 150         MARK1           0              1           0
## 154          MDN1           0              1           0
## 160     MPHOSPH10           0              1           0
## 164         MRPS5           0              1           0
## 166        MYCBP2           0              1           0
## 168         NAT14           0              1           0
## 171       NDUFAF2           0              1           0
## 172        NDUFB9           0              1           0
## 176         NGLY1           0              1           0
## 181          NPC2           0              1           0
## 187         NUP58           0              1           0
## 195          PCNT           0              1           0
## 202        PITRM1           0              1           0
## 204          PLAT           0              1           0
## 208         PLOD2           0              1           0
## 210         PMPCB           0              1           0
## 214           POR           0              1           0
## 218         PRIM2           0              1           0
## 220       PRKAR2A           0              1           0
## 224         PTBP2           0              1           0
## 227           PVR           0              1           0
## 230         RAB14           0              1           0
## 232         RAB1A           0              1           0
## 233         RAB2A           0              1           0
## 242          RBX1           0              1           0
## 245         REEP6           0              1           0
## 248         RIPK1           0              1           0
## 250         RPL36           0              1           0
## 253         SAAL1           0              1           0
## 259       SEPSECS           0              1           0
## 261         SIRT5           0              1           0
## 262      SLC25A21           0              1           0
## 277          STOM           0              1           0
## 290        TIMM8B           0              1           0
## 296       TMEM39B           0              1           0
## 298       TMPRSS2           0              1           0
## 302        TRIM59           0              1           0
## 303         TRMT1           0              1           0
## 304       TUBGCP2           0              1           0
## 307         UBAP2           0              1           0
## 310         UGGT2           0              1           0
## 312         USP54           0              1           0
## 321        ZNF318           0              1           0
##     primate_dginn4
## 19               0
## 23               0
## 31               1
## 32               0
## 37               1
## 40               1
## 47               1
## 48               0
## 67               1
## 68               1
## 72               0
## 75               1
## 80               1
## 83               0
## 101              1
## 105              1
## 110              1
## 111              1
## 112              1
## 118              0
## 119              0
## 125              0
## 127              1
## 131              0
## 143              1
## 144              1
## 145              0
## 150              1
## 154              0
## 160              1
## 164              0
## 166              1
## 168              0
## 171              1
## 172              1
## 176              0
## 181              0
## 187              1
## 195              1
## 202              0
## 204              0
## 208              0
## 210              0
## 214              0
## 218              1
## 220              1
## 224              0
## 227              1
## 230              0
## 232              0
## 233              0
## 242              0
## 245              1
## 248              1
## 250              0
## 253              1
## 259              1
## 261              1
## 262              1
## 277              0
## 290              0
## 296              1
## 298              1
## 302              0
## 303              0
## 304              1
## 307              1
## 310              1
## 312              0
## 321              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{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{1} \hlopt{&amp;} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{0}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
## 14          AKAP9           1              0           1
## 26        ATP6AP1           1              0           1
## 44          CISD3           1              0           1
## 71          EDEM3           1              1           1
## 77         ERGIC1           1              0           1
## 136        IMPDH2           1              0           1
## 137         INHBE           1              0           1
## 231         RAB18           1              0           1
## 239      RAP1GDS1           1              1           1
## 267       SLC44A2           1              0           1
## 283          TBK1           1              0           1
##     primate_dginn4
## 14               0
## 26               0
## 44               0
## 71               0
## 77               0
## 136              0
## 137              0
## 231              0
## 239              0
## 267              0
## 283              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{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{1} \hlopt{&amp;} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{0}\hlstd{,]}
\end{alltt}
\begin{verbatim}
##     tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
## 5           ACAD9           1              0           0
## 11           AGPS           1              0           0
## 14          AKAP9           1              0           1
## 26        ATP6AP1           1              0           1
## 44          CISD3           1              0           1
## 49         COL6A1           1              0           0
## 77         ERGIC1           1              0           1
## 122       GRIPAP1           1              0           0
## 123        GRPEL1           1              0           0
## 136        IMPDH2           1              0           1
## 137         INHBE           1              0           1
## 151         MARK2           1              0           0
## 185        NUP214           1              0           0
## 217         PRIM1           1              0           0
## 226         PUSL1           1              0           0
## 231         RAB18           1              0           1
## 266       SLC30A9           1              0           0
## 267       SLC44A2           1              0           1
## 268      SLC9A3R1           1              0           0
## 283          TBK1           1              0           1
##     primate_dginn4
## 5                0
## 11               0
## 14               0
## 26               0
## 44               0
## 49               0
## 77               0
## 122              0
## 123              0
## 136              0
## 137              0
## 151              0
## 185              0
## 217              0
## 226              0
## 231              0
## 266              0
## 267              0
## 268              0
## 283              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{&lt;-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
\hlstd{tablo}\hlopt{$}\hlstd{nbats}\hlkwb{&lt;-}\hlstd{batstmp}
\hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlkwb{&lt;-}\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{&lt;-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlstd{b} \hlopt{&amp;} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlstd{p]}
    \hlkwa{if}\hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{&gt;}\hlnum{0} \hlopt{&amp;} \hlkwd{length}\hlstd{(tmp)}\hlopt{&lt;=}\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{&gt;}\hlnum{8} \hlopt{&amp;} \hlkwd{length}\hlstd{(tmp)}\hlopt{&lt;=}\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{&gt;}\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{&lt;-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{0} \hlopt{&amp;} \hlstd{tablo}\hlopt{$}\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{&lt;-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{1} \hlopt{&amp;} \hlstd{tablo}\hlopt{$}\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{&lt;-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{0} \hlopt{&amp;} \hlstd{tablo}\hlopt{$}\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{&lt;-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{2} \hlopt{&amp;} \hlstd{tablo}\hlopt{$}\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{$}\hlstd{nbats}\hlopt{&gt;=}\hlnum{3}\hlstd{,}\hlstr{"tmp$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{$}\hlstd{nprimates}\hlopt{&gt;=}\hlnum{3}\hlstd{,}\hlstr{"tmp$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}



\end{document}




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