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Commit 17af5958 authored by mcariou's avatar mcariou
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rerun primate Young

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covid_comp_primate-Young-focus.Rnw
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...@@ -15,7 +15,7 @@ ...@@ -15,7 +15,7 @@
\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis} \title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
\author{Marie Cariou} \author{Marie Cariou}
\date{February 2021} % Activate to display a given date or no date \date{March 2021} % Activate to display a given date or no date
\begin{document} \begin{document}
\maketitle \maketitle
...@@ -29,7 +29,8 @@ ...@@ -29,7 +29,8 @@
\subsection{Complete table} \subsection{Complete table}
<<>>= <<>>=
workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/" home<-"/home/adminmarie/Documents/"
workdir<-paste0(home, "CIRI_BIBS_projects/2020_05_Etienne_covid/")
tab<-read.delim(paste0(workdir, tab<-read.delim(paste0(workdir,
"covid_comp/covid_comp_complete.txt"), h=T, sep="\t") "covid_comp/covid_comp_complete.txt"), h=T, sep="\t")
...@@ -89,48 +90,18 @@ names(tmp)<-c("Gene.name", "NbSites_MEME", "PSS_MEME") ...@@ -89,48 +90,18 @@ names(tmp)<-c("Gene.name", "NbSites_MEME", "PSS_MEME")
tab<-merge(tab, tmp, by="Gene.name") tab<-merge(tab, tmp, by="Gene.name")
dim(tab) dim(tab)
@ @
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Comparisons Primates} \section{Comparisons Primates}
\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results} \subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results}
Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn. Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
<<omegaM7M8>>= <<omegaM7M8>>=
tab$whole.gene.dN.dS.model.0<-as.numeric(as.character(tab$whole.gene.dN.dS.model.0)) tab$whole.gene.dN.dS.model.0<-as.numeric(
as.character(tab$whole.gene.dN.dS.model.0))
plot(tab$whole.gene.dN.dS.model.0, tab$Omega_PamlM7M8, plot(tab$whole.gene.dN.dS.model.0, tab$Omega_PamlM7M8,
xlab="Omega Young-primate", ylab="Omega DGINN-Young-primate") xlab="Omega Young-primate", ylab="Omega DGINN-Young-primate")
abline(0,1) abline(0,1)
...@@ -143,16 +114,16 @@ outlier<-tab[tab$whole.gene.dN.dS.model.0<0.6 & tab$Omega_PamlM7M8>0.7,] ...@@ -143,16 +114,16 @@ outlier<-tab[tab$whole.gene.dN.dS.model.0<0.6 & tab$Omega_PamlM7M8>0.7,]
text(x=outlier$whole.gene.dN.dS.model.0, text(x=outlier$whole.gene.dN.dS.model.0,
y=(outlier$Omega_PamlM7M8+0.01), y=(outlier$Omega_PamlM7M8+0.01),
outlier$Gene.name) outlier$Gene.name)
@ @
\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS DGINN-full's results} \subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS DGINN-full's results}
Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn. Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
<<omegaM7M8_2>>= <<omegaM7M8_2>>=
tab$'dginn.primate_omegaM0Bpp'<-as.numeric(as.character(tab$'dginn.primate_omegaM0Bpp')) tab$'dginn.primate_omegaM0Bpp'<-as.numeric(
as.character(tab$'dginn.primate_omegaM0Bpp'))
plot(tab$'dginn.primate_omegaM0Bpp', tab$Omega_PamlM7M8, plot(tab$'dginn.primate_omegaM0Bpp', tab$Omega_PamlM7M8,
xlab="DGINN-full's", ylab="Omega DGINN-Young-primate") xlab="DGINN-full's", ylab="Omega DGINN-Young-primate")
abline(0,1) abline(0,1)
...@@ -173,72 +144,72 @@ y=(outlier$Omega_PamlM7M8+0.01), ...@@ -173,72 +144,72 @@ y=(outlier$Omega_PamlM7M8+0.01),
outlier$Gene.name) outlier$Gene.name)
@ @
\subsection{Janet Young's results (Young-primate) VS DGINN-full's results} \subsection{Janet Young's results (Young-primate) VS DGINN-full's results}
Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn. Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
<<omegaM7M8_3>>= <<omegaM7M8_3>>=
plot(tab$whole.gene.dN.dS.model.0, as.numeric(as.character(tab$'dginn.primate_omegaM0Bpp')), plot(tab$whole.gene.dN.dS.model.0,
as.numeric(as.character(tab$'dginn.primate_omegaM0Bpp')),
xlab="Omega Young-primate", ylab="DGINN-full's") xlab="Omega Young-primate", ylab="DGINN-full's")
abline(0,1) abline(0,1)
outlier<-tab[tab$whole.gene.dN.dS.model.0<0.4 & as.numeric(as.character(tab$'dginn.primate_omegaM0Bpp'))>0.5,] outlier<-tab[tab$whole.gene.dN.dS.model.0<0.4 &
as.numeric(as.character(tab$'dginn.primate_omegaM0Bpp'))>0.5,]
text(x=outlier$whole.gene.dN.dS.model.0, text(x=outlier$whole.gene.dN.dS.model.0,
y=outlier$'dginn.primate_omegaM0Bpp', y=outlier$'dginn.primate_omegaM0Bpp',
outlier$Gene.name) outlier$Gene.name)
outlier<-tab[tab$whole.gene.dN.dS.model.0>0.7 & as.numeric(as.character(tab$'dginn.primate_omegaM0Bpp'))>0,] outlier<-tab[tab$whole.gene.dN.dS.model.0>0.7 &
as.numeric(as.character(tab$'dginn.primate_omegaM0Bpp'))>0,]
text(x=outlier$whole.gene.dN.dS.model.0, text(x=outlier$whole.gene.dN.dS.model.0,
y=outlier$'dginn.primate_omegaM0Bpp', y=outlier$'dginn.primate_omegaM0Bpp',
outlier$Gene.name) outlier$Gene.name)
outlier<-tab[tab$whole.gene.dN.dS.model.0<0.1 & as.numeric(as.character(tab$'dginn.primate_omegaM0Bpp'))>0.3,] outlier<-tab[tab$whole.gene.dN.dS.model.0<0.1 &
as.numeric(as.character(tab$'dginn.primate_omegaM0Bpp'))>0.3,]
text(x=outlier$whole.gene.dN.dS.model.0+0.03, text(x=outlier$whole.gene.dN.dS.model.0+0.03,
y=outlier$'dginn.primate_omegaM0Bpp', y=outlier$'dginn.primate_omegaM0Bpp',
outlier$Gene.name) outlier$Gene.name)
@ @
\section{Overlap} \section{Overlap}
\subsection{Mondrian} \subsection{Mondrian}
<<mondrianprimates>>= <<mondrianprimates>>=
library(Mondrian) library(Mondrian)
monddata<-as.data.frame(tab$Gene.name) monddata<-as.data.frame(tab$Gene.name)
dim(monddata) dim(monddata)
dginnyoungtmp<-rowSums(cbind(tab$PosSel_PamlM1M2=="Y", tab$PosSel_PamlM7M8=="Y", dginnyoungtmp<-rowSums(cbind(tab$PosSel_PamlM1M2=="Y",
tab$PosSel_BppM1M2=="Y", tab$PosSel_BppM7M8=="Y", tab$PosSel_BUSTED=="Y")) tab$PosSel_PamlM7M8=="Y",
tab$PosSel_BppM1M2=="Y",
#monddata$primates_dginn_young<-ifelse(tmp$PosSel_PamlM7M8=="Y", 1,0) tab$PosSel_BppM7M8=="Y",
tab$PosSel_BUSTED=="Y"))
dginnfulltmp<-rowSums(cbind(tab$'dginn.primate_BUSTED'=="Y", tab$'dginn.primate_BppM1M2'=="Y",
tab$'dginn.primate_BppM7M8'=="Y", tab$'dginn.primate_codemlM1M2'=="Y", tab$'dginn.primate_codemlM7M8'=="Y"))
dginnfulltmp<-rowSums(cbind(tab$'dginn.primate_BUSTED'=="Y",
tab$'dginn.primate_BppM1M2'=="Y",
tab$'dginn.primate_BppM7M8'=="Y",
tab$'dginn.primate_codemlM1M2'=="Y",
tab$'dginn.primate_codemlM7M8'=="Y"))
monddata$primates_young<-ifelse(tab$pVal.M8vsM7<0.05, 1, 0) monddata$primates_young<-ifelse(tab$pVal.M8vsM7<0.05, 1, 0)
#monddata$primates_cooper<-ifelse(tab$cooper.primates.M7.M8_p_val<0.05, 1, 0)
monddata$primates_dginn_young<-ifelse(dginnyoungtmp>=3, 1,0) monddata$primates_dginn_young<-ifelse(dginnyoungtmp>=3, 1,0)
monddata$primates_dginn_full<-ifelse(dginnfulltmp>=3, 1,0) monddata$primates_dginn_full<-ifelse(dginnfulltmp>=3, 1,0)
mondrian(na.omit(monddata[,2:4]), labels=c("Young", "DGINN-Young >=3", "DGINN-full >=3" )) mondrian(na.omit(monddata[,2:4]),
labels=c("Young", "DGINN-Young >=3", "DGINN-full >=3" ))
#####
monddata$primates_dginn_young<-ifelse(dginnyoungtmp>=4, 1,0) monddata$primates_dginn_young<-ifelse(dginnyoungtmp>=4, 1,0)
monddata$primates_dginn_full<-ifelse(dginnfulltmp>=4, 1,0) monddata$primates_dginn_full<-ifelse(dginnfulltmp>=4, 1,0)
mondrian(na.omit(monddata[,2:4]), labels=c("Young", "DGINN-Young >=4", "DGINN-full >=4")) mondrian(na.omit(monddata[,2:4]),
labels=c("Young", "DGINN-Young >=4", "DGINN-full >=4"))
@ @
Comparison of results with the same method. Comparison of results with the same method.
...@@ -246,7 +217,9 @@ Comparison of results with the same method. ...@@ -246,7 +217,9 @@ Comparison of results with the same method.
monddata$primates_dginn_young<-tab$PosSel_BppM7M8=="Y" monddata$primates_dginn_young<-tab$PosSel_BppM7M8=="Y"
monddata$primates_dginn_full<-tab$'dginn.primate_codemlM7M8'=="Y" monddata$primates_dginn_full<-tab$'dginn.primate_codemlM7M8'=="Y"
mondrian(na.omit(monddata[,2:4]), labels=c("Young", "DGINN-Young", "DGINN-full"), main="posel codeml M7M8") mondrian(na.omit(monddata[,2:4]),
labels=c("Young", "DGINN-Young", "DGINN-full"),
main="posel codeml M7M8")
@ @
\subsection{subsetR} \subsection{subsetR}
......
covid_comp_primate-Young-focus.pdf
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covid_comp_primate-Young-focus.tex
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View file @ 17af5958
...@@ -65,7 +65,7 @@ ...@@ -65,7 +65,7 @@
\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis} \title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
\author{Marie Cariou} \author{Marie Cariou}
\date{February 2021} % Activate to display a given date or no date \date{March 2021} % Activate to display a given date or no date
\IfFileExists{upquote.sty}{\usepackage{upquote}}{} \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document} \begin{document}
\maketitle \maketitle
...@@ -81,7 +81,8 @@ ...@@ -81,7 +81,8 @@
\begin{knitrout} \begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt} \begin{alltt}
\hlstd{workdir}\hlkwb{<-}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"} \hlstd{home}\hlkwb{<-}\hlstr{"/home/adminmarie/Documents/"}
\hlstd{workdir}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"CIRI_BIBS_projects/2020_05_Etienne_covid/"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \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{)} \hlstr{"covid_comp/covid_comp_complete.txt"}\hlstd{),} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
...@@ -168,46 +169,17 @@ I will merge the 2 tables. ...@@ -168,46 +169,17 @@ I will merge the 2 tables.
\end{knitrout} \end{knitrout}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Comparisons Primates} \section{Comparisons Primates}
\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results} \subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results}
Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn. Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
\begin{knitrout} \begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt} \begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0))} \hlstd{tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}
\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0))}
\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0, tab}\hlopt{$}\hlstd{Omega_PamlM7M8,} \hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0, tab}\hlopt{$}\hlstd{Omega_PamlM7M8,}
\hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-Young-primate"}\hlstd{)} \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-Young-primate"}\hlstd{)}
\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)} \hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}
...@@ -228,12 +200,13 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d ...@@ -228,12 +200,13 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d
\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS DGINN-full's results} \subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS DGINN-full's results}
Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn. Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
\begin{knitrout} \begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt} \begin{alltt}
\hlstd{tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))} \hlstd{tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}
\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}
\end{alltt} \end{alltt}
...@@ -262,30 +235,33 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d ...@@ -262,30 +235,33 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d
\end{knitrout} \end{knitrout}
\subsection{Janet Young's results (Young-primate) VS DGINN-full's results} \subsection{Janet Young's results (Young-primate) VS DGINN-full's results}
Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn. Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
\begin{knitrout} \begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt} \begin{alltt}
\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{)),} \hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{)),}
\hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"DGINN-full's"}\hlstd{)} \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"DGINN-full's"}\hlstd{)}
\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)} \hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}
\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}\hlopt{>}\hlnum{0.5}\hlstd{,]} \hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.4} \hlopt{&}
\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}\hlopt{>}\hlnum{0.5}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,} \hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{,} \hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{,}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)} \hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{>}\hlnum{0.7} \hlopt{&} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}\hlopt{>}\hlnum{0}\hlstd{,]} \hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{>}\hlnum{0.7} \hlopt{&}
\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}\hlopt{>}\hlnum{0}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,} \hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{,} \hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{,}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)} \hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.1} \hlopt{&} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}\hlopt{>}\hlnum{0.3}\hlstd{,]} \hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.1} \hlopt{&}
\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}\hlopt{>}\hlnum{0.3}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{+}\hlnum{0.03}\hlstd{,} \hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{+}\hlnum{0.03}\hlstd{,}
\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{,} \hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{,}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)} \hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
...@@ -295,10 +271,8 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d ...@@ -295,10 +271,8 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d
\end{knitrout} \end{knitrout}
\section{Overlap} \section{Overlap}
\subsection{Mondrian} \subsection{Mondrian}
\begin{knitrout} \begin{knitrout}
...@@ -313,33 +287,34 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d ...@@ -313,33 +287,34 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d
## [1] 332 1 ## [1] 332 1
\end{verbatim} \end{verbatim}
\begin{alltt} \begin{alltt}
\hlstd{dginnyoungtmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstd{PosSel_PamlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,} \hlstd{dginnyoungtmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstd{PosSel_PamlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstd{PosSel_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{PosSel_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{PosSel_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{))} \hlstd{tab}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstd{PosSel_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlcom{#monddata$primates_dginn_young<-ifelse(tmp$PosSel_PamlM7M8=="Y", 1,0)} \hlstd{tab}\hlopt{$}\hlstd{PosSel_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstd{PosSel_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{))}
\hlstd{dginnfulltmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_BUSTED'}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstr{'dginn.primate_BppM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{,} \hlstd{dginnfulltmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_BUSTED'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstr{'dginn.primate_BppM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstr{'dginn.primate_codemlM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstr{'dginn.primate_codemlM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{))} \hlstd{tab}\hlopt{$}\hlstr{'dginn.primate_BppM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstr{'dginn.primate_BppM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstr{'dginn.primate_codemlM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstr{'dginn.primate_codemlM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{))}
\hlstd{monddata}\hlopt{$}\hlstd{primates_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)} \hlstd{monddata}\hlopt{$}\hlstd{primates_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
\hlcom{#monddata$primates_cooper<-ifelse(tab$cooper.primates.M7.M8_p_val<0.05, 1, 0)}
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)} \hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)} \hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young >=3"}\hlstd{,} \hlstr{"DGINN-full >=3"} \hlstd{))} \hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),}
\hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young >=3"}\hlstd{,} \hlstr{"DGINN-full >=3"} \hlstd{))}
\end{alltt} \end{alltt}
\end{kframe} \end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianprimates-1} \includegraphics[width=\maxwidth]{figure/mondrianprimates-1}
\begin{kframe}\begin{alltt} \begin{kframe}\begin{alltt}
\hlcom{#####}
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)} \hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)} \hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young >=4"}\hlstd{,} \hlstr{"DGINN-full >=4"}\hlstd{))} \hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),}
\hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young >=4"}\hlstd{,} \hlstr{"DGINN-full >=4"}\hlstd{))}
\end{alltt} \end{alltt}
\end{kframe} \end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianprimates-2} \includegraphics[width=\maxwidth]{figure/mondrianprimates-2}
...@@ -353,7 +328,9 @@ Comparison of results with the same method. ...@@ -353,7 +328,9 @@ Comparison of results with the same method.
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlstd{tab}\hlopt{$}\hlstd{PosSel_BppM7M8}\hlopt{==}\hlstr{"Y"} \hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlstd{tab}\hlopt{$}\hlstd{PosSel_BppM7M8}\hlopt{==}\hlstr{"Y"}
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlstd{tab}\hlopt{$}\hlstr{'dginn.primate_codemlM7M8'}\hlopt{==}\hlstr{"Y"} \hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlstd{tab}\hlopt{$}\hlstr{'dginn.primate_codemlM7M8'}\hlopt{==}\hlstr{"Y"}
\hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young"}\hlstd{,} \hlstr{"DGINN-full"}\hlstd{),} \hlkwc{main}\hlstd{=}\hlstr{"posel codeml M7M8"}\hlstd{)} \hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),}
\hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young"}\hlstd{,} \hlstr{"DGINN-full"}\hlstd{),}
\hlkwc{main}\hlstd{=}\hlstr{"posel codeml M7M8"}\hlstd{)}
\end{alltt} \end{alltt}
\end{kframe} \end{kframe}
\includegraphics[width=\maxwidth]{figure/unnamed-chunk-4-1} \includegraphics[width=\maxwidth]{figure/unnamed-chunk-4-1}
...@@ -500,7 +477,7 @@ List of the 44 genes found under positive selection ONLY in full-DGINN. ...@@ -500,7 +477,7 @@ List of the 44 genes found under positive selection ONLY in full-DGINN.
## [29] MYCBP2 NAT14 NGLY1 NPC2 NUPL1 PITRM1 PLOD2 ## [29] MYCBP2 NAT14 NGLY1 NPC2 NUPL1 PITRM1 PLOD2
## [36] PMPCB POR PRKAR2A PTBP2 RAB14 RAB1A RAB2A ## [36] PMPCB POR PRKAR2A PTBP2 RAB14 RAB1A RAB2A
## [43] RAP1GDS1 RBX1 REEP6 RPL36 SCCPDH <NA> <NA> ## [43] RAP1GDS1 RBX1 REEP6 RPL36 SCCPDH <NA> <NA>
## [50] TIMM8B TRIM59 TUBGCP2 <NA> <NA> ## [50] TIMM8B TRIM59 TUBGCP2 <NA>
## 332 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACSL3 ADAM9 ... ZYG11B ## 332 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACSL3 ADAM9 ... ZYG11B
\end{verbatim} \end{verbatim}
\end{kframe} \end{kframe}
......
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