\documentclass[11pt, oneside]{article}\usepackage[]{graphicx}\usepackage[]{color} % maxwidth is the original width if it is less than linewidth % otherwise use linewidth (to make sure the graphics do not exceed the margin) \makeatletter \def\maxwidth{ % \ifdim\Gin@nat@width>\linewidth \linewidth \else \Gin@nat@width \fi } \makeatother
\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345} \newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}% \newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}% \newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}% \newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}% \newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}% \newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}% \newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}% \newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}% \newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}% \let\hlipl\hlkwb
\usepackage{framed} \makeatletter \newenvironment{kframe}{% \def\at@end@of@kframe{}% \ifinner\ifhmode% \def\at@end@of@kframe{\end{minipage}}% \begin{minipage}{\columnwidth}% \fi\fi% \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep \colorbox{shadecolor}{##1}\hskip-\fboxsep % There is no \@totalrightmargin, so: \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}% \MakeFramed {\advance\hsize-\width \@totalleftmargin\z@ \linewidth\hsize \@setminipage}}% {\par\unskip\endMakeFramed% \at@end@of@kframe} \makeatother
\definecolor{shadecolor}{rgb}{.97, .97, .97} \definecolor{messagecolor}{rgb}{0, 0, 0} \definecolor{warningcolor}{rgb}{1, 0, 1} \definecolor{errorcolor}{rgb}{1, 0, 0} \newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
\usepackage{alltt} % use “amsart” instead of “article” for AMSLaTeX format
%\usepackage{geometry} % See geometry.pdf to learn the layout options. There are lots.
%\geometry{letterpaper} % … or a4paper or a5paper or …
%\geometry{landscape} % Activate for for rotated page geometry
%\usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
%\usepackage{graphicx} % Use pdf, png, jpg, or eps with pdflatex; use eps in DVI mode
% TeX will automatically convert eps –> pdf in pdflatex
%\usepackage{amssymb}
\usepackage[utf8]{inputenc} %\usepackage[cyr]{aeguill} %\usepackage[francais]{babel} %\usepackage{hyperref}
\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis} \author{Marie Cariou} \date{Janvier 2021} % Activate to display a given date or no date \IfFileExists{upquote.sty}{\usepackage{upquote}}{} \begin{document} \maketitle
\tableofcontents
\newpage
\section{Files manipulations}
\subsection{Read Janet Young's table}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{workdir}\hlkwb{<-}\hlstr{“/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/”}
\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{“data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv”}\hlstd{),} \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{dec}\hlstd{=}\hlstr{“,”}\hlstd{)} \hlkwd{dim}\hlstd{(tab)} \end{alltt} \begin{verbatim}
\end{verbatim} \end{kframe} \end{knitrout}
\subsection{Read DGINN Young table}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{dginnY}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{“data/summary_primate_young.res”}\hlstd{),} \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
\hlkwd{dim}\hlstd{(dginnY)} \end{alltt} \begin{verbatim}
\end{verbatim} \end{kframe} \end{knitrout}
\subsection{Joining Young and DGINN Young table}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlcom{# correct gene names (MARC1)} \hlstd{val_remp}\hlkwb{=}\hlkwd{as.character}\hlstd{(}\hlkwd{unique}\hlstd{(dginnY}\hlopt{\(}\hlstd{Gene)[(}\hlkwd{unique}\hlstd{(dginnY}\hlopt{\)}\hlstd{Gene)} \hlopt{%in%} \hlstd{tab}\hlopt{\(}\hlstd{Gene.name)}\hlopt{==}\hlstd{F])} \hlstd{tab}\hlopt{\)}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{\(}\hlstd{Gene.name)} \hlstd{tab}\hlopt{\)}\hlstd{Gene.name[}\hlnum{158}\hlstd{]}\hlkwb{<-}\hlstd{val_remp} \hlkwd{sum}\hlstd{(}\hlkwd{unique}\hlstd{(dginnY}\hlopt{\(}\hlstd{Gene)} \hlopt{%in%} \hlkwd{unique}\hlstd{(tab}\hlopt{\)}\hlstd{Gene.name))} \end{alltt} \begin{verbatim}
\end{verbatim} \end{kframe} \end{knitrout}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{add_col}\hlkwb{<-}\hlkwa{function}\hlstd{(}\hlkwc{method}\hlstd{=}\hlstr{“PamlM1M2”}\hlstd{){}
\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstd{method,} \hlkwd{c}\hlstd{(}\hlstr{“Gene”}\hlstd{,} \hlstr{“Omega”}\hlstd{,} \hlstr{“PosSel”}\hlstd{,} \hlstr{“PValue”}\hlstd{,} \hlstr{“NbSites”}\hlstd{,} \hlstr{“PSS”}\hlstd{)]}
\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“Gene.name”}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{“Omega”}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{“PosSel”}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{“PValue”}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{“NbSites”}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{“PSS_”}\hlstd{, method))}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{“Gene.name”}\hlstd{)}
\hlkwd{return}\hlstd{(tab)} \hlstd{}}
\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{“PamlM1M2”}\hlstd{)} \hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{“PamlM7M8”}\hlstd{)} \hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{“BppM1M2”}\hlstd{)} \hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{“BppM7M8”}\hlstd{)}
\hlcom{# Manip pour la colonne BUSTED}
\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{“BUSTED”}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{“Gene”}\hlstd{,} \hlstr{“Omega”}\hlstd{,} \hlstr{“PosSel”}\hlstd{,} \hlstr{“PValue”}\hlstd{)]} \hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“Gene.name”}\hlstd{,} \hlstr{“Omega_BUSTED”}\hlstd{,} \hlstr{“PosSel_BUSTED”}\hlstd{,} \hlstr{“PValue_BUSTED”}\hlstd{)} \hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{“Gene.name”}\hlstd{)}
\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{“MEME”}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{“Gene”}\hlstd{,} \hlstr{“NbSites”}\hlstd{,} \hlstr{“PSS”}\hlstd{)]} \hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“Gene.name”}\hlstd{,} \hlstr{“NbSites_MEME”}\hlstd{,} \hlstr{“PSS_MEME”}\hlstd{)} \hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{“Gene.name”}\hlstd{)} \end{alltt} \end{kframe} \end{knitrout}
\subsection{Read DGINN Table}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{dginnT}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{“data/DGINN_202005281649summary_cleaned.csv”}\hlstd{),} \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{“,”}\hlstd{)}
\hlkwd{dim}\hlstd{(dginnT)} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlkwd{names}\hlstd{(dginnT)} \end{alltt} \begin{verbatim}
\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}
\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}
\end{verbatim} \begin{alltt} \hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“File”}\hlstd{,} \hlstr{“Name”}\hlstd{,} \hlstr{“Gene.name”}\hlstd{,} \hlstr{“GeneSize”}\hlstd{,} \hlstr{“dginn-primate_NbSpecies”}\hlstd{,} \hlstr{“dginn-primate_omegaM0Bpp”}\hlstd{,} \hlstr{“dginn-primate_omegaM0codeml”}\hlstd{,} \hlstr{“dginn-primate_BUSTED”}\hlstd{,} \hlstr{“dginn-primate_BUSTED.p.value”}\hlstd{,} \hlstr{“dginn-primate_MEME.NbSites”}\hlstd{,} \hlstr{“dginn-primate_MEME.PSS”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2.p.value”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2.NbSites”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2.PSS”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8.p.value”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8.NbSites”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8.PSS”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2.p.value”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2.NbSites”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2.PSS”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8.p.value”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8.NbSites”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8.PSS”}\hlstd{)} \end{alltt} \end{kframe} \end{knitrout}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{table}\hlstd{(dginnT}\hlopt{\(}\hlstd{dginn-primate_BUSTED)}
\hlkwd{table}\hlstd{(dginnT}\hlopt{\)}\hlstd{dginn-primate_codemlM1M2)}
\hlkwd{table}\hlstd{(dginnT}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8)}
\hlkwd{table}\hlstd{(dginnT}\hlopt{\)}\hlstd{dginn-primate_BppM1M2)}
\hlkwd{table}\hlstd{(dginnT}\hlopt{$}\hlstd{dginn-primate_BppM7M8)}
\hlkwd{table}\hlstd{(dginnT}\hlopt{\(}\hlstd{dginn-primate_BUSTED}\hlopt{==}\hlstr{“na”}\hlstd{,dginnT}\hlopt{\)}\hlstd{dginn-primate_codemlM1M2}\hlopt{==}\hlstr{“na”}\hlstd{, dginnT}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8}\hlopt{==}\hlstr{“na”}\hlstd{,}
\hlstd{dginnT}\hlopt{\)}\hlstd{dginn-primate_BppM1M2}\hlopt{==}\hlstr{“na”}\hlstd{, dginnT}\hlopt{$}\hlstd{dginn-primate_BppM7M8}\hlopt{==}\hlstr{“na”} \hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
\subsection{Join Table and DGINN table}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnT,} \hlkwc{by}\hlstd{=}\hlstr{“Gene.name”}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{dginn-primate_BUSTED)}
\end{alltt}
\begin{verbatim}
\end{verbatim}
\begin{alltt}
\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{dginn-primate_codemlM1M2)}
\end{alltt}
\begin{verbatim}
\end{verbatim}
\begin{alltt}
\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{dginn-primate_codemlM7M8)}
\end{alltt}
\begin{verbatim}
\end{verbatim}
\begin{alltt}
\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{dginn-primate_BppM1M2)}
\end{alltt}
\begin{verbatim}
\end{verbatim}
\begin{alltt}
\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{dginn-primate_BppM7M8)}
\end{alltt}
\begin{verbatim}
\end{verbatim}
\begin{alltt}
\hlkwd{table}\hlstd{(tab}\hlopt{\(}\hlstd{dginn-primate_BUSTED}\hlopt{==}\hlstr{“na”} \hlopt{|} \hlstd{tab}\hlopt{\)}\hlstd{dginn-primate_codemlM1M2}\hlopt{==}\hlstr{“na”} \hlopt{|} \hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8}\hlopt{==}\hlstr{“na”} \hlopt{|}
\hlstd{tab}\hlopt{\)}\hlstd{dginn-primate_BppM1M2}\hlopt{==}\hlstr{“na”}\hlopt{|} \hlstd{tab}\hlopt{$}\hlstd{dginn-primate_BppM7M8}\hlopt{==}\hlstr{“na”} \hlstd{)}
\end{alltt}
\begin{verbatim}
\end{verbatim} \end{kframe} \end{knitrout}
\subsection{Add DGINN results on bat dataset}
DGINN results from different analysis.
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlcom{# original table} \hlstd{dginnbats}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{“data/DGINN_202005281339summary_cleaned.tab”}\hlstd{),} \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
\hlcom{# rerun on corrected alignment} \hlstd{dginnbatsnew1}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{“data/DGINN_202011262248_summary.tab”}\hlstd{),} \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)} \hlstd{dginnbatsnew2}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{“data/DGINN_202012192053_summary.tab”}\hlstd{),} \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
\hlcom{# colomne choice, BUSTED and Bppml form first file, codeml from the other one} \hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew1} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{omegaM0codeml}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{omegaM0codeml}
\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM1M2}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM1M2} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM1M2_p.value}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM1M2_p.value} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM1M2_NbSites}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM1M2_NbSites} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM1M2_PSS}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM1M2_PSS}
\hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM7M8}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM7M8} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM7M8_p.value}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM7M8_p.value} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM7M8_NbSites}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM7M8_NbSites} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{codemlM7M8_PSS}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{\)}\hlstd{codemlM7M8_PSS}
\hlcom{####}
\hlcom{## RIPK1 is actually a primat results}
\hlcom{## 1. Take it and put it at the right place}
\hlstd{ripk1}\hlkwb{<-}\hlkwd{as.vector}\hlstd{(dginnbatsnew[dginnbatsnew}\hlopt{\(}\hlstd{Gene}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,])}
\hlstd{tab}\hlopt{\)}\hlstd{dginn-primate_omegaM0Bpp}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{dginn-primate_omegaM0Bpp))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_BUSTED.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{dginn-primate_BUSTED.p.value))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_BppM1M2.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{dginn-primate_BppM1M2.p.value))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_BppM7M8.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{dginn-primate_BppM7M8.p.value))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_BppM7M8.PSS}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{dginn-primate_BppM7M8.PSS))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM1M2.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{dginn-primate_codemlM1M2.p.value))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM1M2.PSS}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{dginn-primate_codemlM1M2.PSS))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{dginn-primate_codemlM7M8.p.value))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{\(}\hlstd{dginn-primate_codemlM7M8.PSS}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{\)}\hlstd{dginn-primate_codemlM7M8.PSS))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“GeneSize”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{GeneSize} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_NbSpecies"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{NbSpecies} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_omegaM0Bpp"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{omegaM0Bpp} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_omegaM0codeml"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{omegaM0codeml}
\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“dginn-primate_BUSTED”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BUSTED} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BUSTED.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BUSTED_p.value} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_MEME.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{MEME_NbSites} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_MEME.PSS"}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ripk1}\hlopt{\)}\hlstd{MEME_PSS))} \end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“dginn-primate_BppM1M2”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM1M2} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM1M2_p.value} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM1M2_NbSites} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM1M2_PSS}
\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“dginn-primate_BppM7M8”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM7M8} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM7M8_p.value} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM7M8_NbSites} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{BppM7M8_PSS}
\hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlstr{“dginn-primate_codemlM1M2”}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM1M2} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM1M2_p.value} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM1M2_NbSites} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM1M2_PSS} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM7M8} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM7M8_p.value} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM7M8_NbSites} \hlstd{tab[tab}\hlopt{\(}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{\)}\hlstd{codemlM7M8_PSS}
\hlcom{## 2. Remove it} \hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{!=}\hlstr{“RIPK1”}\hlstd{,]}
\hlcom{## suppress redundant lines} \hlstd{dginnbats}\hlkwb{<-}\hlstd{dginnbats[(dginnbats}\hlopt{\(}\hlstd{Gene} \hlopt{%in%} \hlstd{dginnbatsnew}\hlopt{\)}\hlstd{Gene)}\hlopt{==}\hlnum{FALSE}\hlstd{,]} \hlkwd{names}\hlstd{(dginnbatsnew)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnbats)}
\hlcom{##############“} \hlstd{dginnbatsnew[,}\hlnum{4}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(dginnbatsnew[,}\hlnum{4}\hlstd{])} \hlstd{dginnbats[,}\hlnum{6}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{6}\hlstd{]))} \end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt} \hlstd{dginnbats[,}\hlnum{8}\hlstd{]}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{8}\hlstd{])} \hlstd{dginnbats[,}\hlnum{12}\hlstd{]}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{12}\hlstd{])} \hlstd{dginnbats[,}\hlnum{13}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{13}\hlstd{]))} \end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt} \hlstd{dginnbats[,}\hlnum{16}\hlstd{]}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{16}\hlstd{])} \hlstd{dginnbats[,}\hlnum{17}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{17}\hlstd{]))} \end{alltt}
{\ttfamily\noindent\color{warningcolor}{## Warning: NAs introduits lors de la conversion automatique}}\begin{alltt} \hlcom{## replace by new data} \hlstd{dginnbats}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnbats, dginnbatsnew)}
\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File”}\hlstd{,} \hlstr{“batsName”}\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}
\end{verbatim} \begin{alltt} \hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnbats,} \hlkwc{by}\hlstd{=}\hlstr{“cooper.batsGene”}\hlstd{,} \hlkwc{all.x}\hlstd{=T)} \end{alltt} \end{kframe} \end{knitrout}
\subsection{Write the new table}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlkwd{write.table}\hlstd{(tab,} \hlstr{“covid_comp_complete.txt”}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{“\textbackslash{}t”}\hlstd{)} \end{alltt} \end{kframe} \end{knitrout}
\section{Second Table}
Table containing the DGINN results for both Primates and bats. Conserve all genes.
\subsection{Primates}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{dginnT}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{“data/DGINN_202005281649summary_cleaned.csv”}\hlstd{),} \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{“,”}\hlstd{)}
\hlkwd{dim}\hlstd{(dginnT)} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlkwd{names}\hlstd{(dginnT)} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlcom{# Rename the columns to include primate} \hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“File”}\hlstd{,} \hlstr{“Name”}\hlstd{,} \hlstr{“Gene.name”}\hlstd{,} \hlstr{“GeneSize”}\hlstd{,} \hlstr{“dginn-primate_NbSpecies”}\hlstd{,} \hlstr{“dginn-primate_omegaM0Bpp”}\hlstd{,} \hlstr{“dginn-primate_omegaM0codeml”}\hlstd{,} \hlstr{“dginn-primate_BUSTED”}\hlstd{,} \hlstr{“dginn-primate_BUSTED.p.value”}\hlstd{,} \hlstr{“dginn-primate_MEME.NbSites”}\hlstd{,} \hlstr{“dginn-primate_MEME.PSS”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2.p.value”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2.NbSites”}\hlstd{,} \hlstr{“dginn-primate_BppM1M2.PSS”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8.p.value”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8.NbSites”}\hlstd{,} \hlstr{“dginn-primate_BppM7M8.PSS”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2.p.value”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2.NbSites”}\hlstd{,} \hlstr{“dginn-primate_codemlM1M2.PSS”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8.p.value”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8.NbSites”}\hlstd{,} \hlstr{“dginn-primate_codemlM7M8.PSS”}\hlstd{)} \end{alltt} \end{kframe} \end{knitrout}
\subsection{Bats}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlcom{# original table} \hlstd{dginnbats}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{“data/DGINN_202005281339summary_cleaned-LE201108.txt”}\hlstd{),} \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
\hlcom{# rerun on corrected alignment} \hlstd{dginnbatsnew}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{“data/DGINN_202011262248_hyphybpp-202012192053_codeml-summary.txt”}\hlstd{),} \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)} \end{alltt} \end{kframe} \end{knitrout} \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlcom{# Add both columns } \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{Lucie.s.comments}\hlkwb{<-}\hlstr{""} \hlstd{dginnbatsnew}\hlopt{\)}\hlstd{Action.taken}\hlkwb{<-}\hlstr{""}
\hlcom{# Homogenize column names} \hlstd{dginnbats}\hlopt{\(}\hlstd{BUSTED_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BUSTED.p.value} \hlstd{dginnbats}\hlopt{\(}\hlstd{MEME_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{MEME.NbSites} \hlstd{dginnbats}\hlopt{\(}\hlstd{MEME_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{MEME.PSS}
\hlstd{dginnbats}\hlopt{\(}\hlstd{BppM1M2_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM1M2.p.value} \hlstd{dginnbats}\hlopt{\(}\hlstd{BppM1M2_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM1M2.NbSites} \hlstd{dginnbats}\hlopt{\(}\hlstd{BppM1M2_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM1M2.PSS}
\hlstd{dginnbats}\hlopt{\(}\hlstd{BppM7M8_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM7M8.p.value} \hlstd{dginnbats}\hlopt{\(}\hlstd{BppM7M8_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM7M8.NbSites} \hlstd{dginnbats}\hlopt{\(}\hlstd{BppM7M8_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{BppM7M8.PSS}
\hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM1M2_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM1M2.p.value} \hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM1M2_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM1M2.NbSites} \hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM1M2_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM1M2.PSS}
\hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM7M8_p.value}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM7M8.p.value} \hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM7M8_NbSites}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM7M8.NbSites} \hlstd{dginnbats}\hlopt{\(}\hlstd{codemlM7M8_PSS}\hlkwb{<-}\hlstd{dginnbats}\hlopt{\)}\hlstd{codemlM7M8.PSS} \end{alltt} \end{kframe} \end{knitrout}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlcom{# Order columns in the same order in both tables} \hlstd{dginnbats}\hlkwb{<-}\hlstd{dginnbats[,}\hlkwd{names}\hlstd{(dginnbatsnew)]}
\hlkwd{names}\hlstd{(dginnbatsnew)} \hlopt{%in%} \hlkwd{names}\hlstd{(dginnbats)} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlkwd{names}\hlstd{(dginnbats)}\hlopt{==}\hlkwd{names}\hlstd{(dginnbatsnew)} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlcom{# Put RIPK aside} \hlstd{ripk1}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{==}\hlstr{“RIPK1”}\hlstd{,}\hlnum{1}\hlopt{:}\hlnum{27}\hlstd{]}
\hlcom{# Add it to primate table} \hlkwd{names}\hlstd{(ripk1)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnT)}
\hlstd{ripk1}\hlopt{\(}\hlstd{dginn-primate_omegaM0Bpp}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{\)}\hlstd{dginn-primate_omegaM0Bpp)}
\hlstd{ripk1}\hlopt{\(}\hlstd{dginn-primate_BUSTED.p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{\)}\hlstd{dginn-primate_BUSTED.p.value)}
\hlstd{ripk1}\hlopt{\(}\hlstd{dginn-primate_BppM1M2.p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{\)}\hlstd{dginn-primate_BppM1M2.p.value)}
\hlstd{ripk1}\hlopt{\(}\hlstd{dginn-primate_BppM7M8.p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(ripk1}\hlopt{\)}\hlstd{dginn-primate_BppM7M8.p.value)}
\hlstd{dginnT}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnT, ripk1)}
\hlcom{## Remove it Ripk1 from bats} \hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{!=}\hlstr{“RIPK1”}\hlstd{,]}
\hlcom{## suppress redundant lines} \hlstd{dginnbats}\hlkwb{<-}\hlstd{dginnbats[(dginnbats}\hlopt{\(}\hlstd{Gene} \hlopt{%in%} \hlstd{dginnbatsnew}\hlopt{\)}\hlstd{Gene)}\hlopt{==}\hlnum{FALSE}\hlstd{,]} \hlkwd{names}\hlstd{(dginnbatsnew)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnbats)}
\hlcom{## replace by new data} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{omegaM0Bpp}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(dginnbatsnew}\hlopt{\)}\hlstd{omegaM0Bpp)} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{BppM1M2_p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(dginnbatsnew}\hlopt{\)}\hlstd{BppM1M2_p.value)} \hlstd{dginnbatsnew}\hlopt{\(}\hlstd{BppM7M8_p.value}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(dginnbatsnew}\hlopt{\)}\hlstd{BppM7M8_p.value)}
\hlstd{dginnbats}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnbats, dginnbatsnew)}
\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{“batsFile”}\hlstd{,} \hlstr{“bats_Name”}\hlstd{,} \hlstr{“Gene.name”}\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}
\end{verbatim} \end{kframe} \end{knitrout}
\subsection{Merged table}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{tidy.opts} \hlkwb{=} \hlkwd{list}\hlstd{(}\hlkwc{width.cutoff} \hlstd{=} \hlnum{30}\hlstd{)} \hlkwd{dim}\hlstd{(dginnT)} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlkwd{dim}\hlstd{(dginnbats)} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name} \end{alltt} \begin{verbatim}
\end{verbatim} \end{kframe} \end{knitrout}
\begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlcom{# genes in common} \hlstd{dginnT}\hlopt{\(}\hlstd{Gene.name[dginnT}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name]} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlkwd{length}\hlstd{(dginnT}\hlopt{\(}\hlstd{Gene.name[dginnT}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name])} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlcom{# genes only in primates} \hlstd{dginnT}\hlopt{\(}\hlstd{Gene.name[(dginnT}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlkwd{length}\hlstd{(dginnT}\hlopt{\(}\hlstd{Gene.name[(dginnT}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlcom{# genes only in bats} \hlstd{dginnbats}\hlopt{\(}\hlstd{Gene.name[(dginnbats}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]} \end{alltt} \begin{verbatim}
\end{verbatim} \begin{alltt} \hlkwd{length}\hlstd{(dginnbats}\hlopt{\(}\hlstd{Gene.name[(dginnbats}\hlopt{\)}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])} \end{alltt} \begin{verbatim}
\end{verbatim} \end{kframe} \end{knitrout}
\end{document}