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-\documentclass[11pt, oneside]{article} % 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{Mai 2020} % Activate to display a given date or no date
-
-\begin{document}
-\maketitle
-
-\tableofcontents
-
-\newpage
-
-\section{Files manipulations}
-
-I will compare Janet Young's results to DGINN results, on the SAME alignment.
-
-\subsection{Read Janet Young's table}
-
-<<>>=
-tab<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv",
- fill=T, h=T, dec=",")
-dim(tab)
-
-names(tab)
-
-@
-
-\subsection{Read DGINN table}
-
-<<>>=
-dginn<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/summary.res",
- fill=T, h=T)
-
-dim(dginn)
-
-names(dginn)
-@
-
-\subsection{Joining table}
-
-\subsubsection{Based on which column?}
-
-<<>>=
-head(tab)[,1:5]
-# gene avec un nom bizar dans certaines colomne
-tab[158,1:10]
-
-#
-length(unique(dginn$Gene))
-length(unique(tab$PreyGene))
-length(unique(tab$Gene.name))
-
-#quelle paire de colonne contient le plus de noms identiques
-sum(unique(dginn$Gene) %in% unique(tab$PreyGene))
-sum(unique(dginn$Gene) %in% unique(tab$Gene.name))
-
-# dginn$Gene et tab$Gene.name presque identiques sauf 1 ligne.
-# Je soupçonne que c'est celle là :
-tab[158,1:10]
-
-# Verif:
-tab[,1:10][(tab$Gene.name %in% unique(dginn$Gene))==F,]
-# yep
-
-# Remplacement manuel par
-as.character(unique(dginn$Gene)[(unique(dginn$Gene) %in% tab$Gene.name)==F])
-# dans le tableau de Janet
-
-val_remp=as.character(unique(dginn$Gene)[(unique(dginn$Gene) %in% tab$Gene.name)==F])
-
-tab$Gene.name<-as.character(tab$Gene.name)
-
-tab$Gene.name[158]<-val_remp
-
-sum(unique(dginn$Gene) %in% unique(tab$Gene.name))
-@
-
-\subsubsection{New columns}
-
-<<>>=
-
-add_col<-function(method="PamlM1M2"){
-
-tmp<-dginn[dginn$Method==method,
- c("Gene", "Omega", "PosSel", "PValue", "NbSites", "PSS")]
-
-names(tmp)<-c("Gene.name", paste0("Omega_", method),
- paste0("PosSel_", method), paste0("PValue_", method),
- paste0("NbSites_", method), paste0("PSS_", method))
-
-tab<-merge(tab, tmp, by="Gene.name")
-
-return(tab)
-}
-
-tab<-add_col("PamlM1M2")
-tab<-add_col("PamlM7M8")
-tab<-add_col("BppM1M2")
-tab<-add_col("BppM7M8")
-
-
-# Manip pour la colonne BUSTED
-
-tmp<-dginn[dginn$Method=="BUSTED",c("Gene", "Omega", "PosSel", "PValue")]
-names(tmp)<-c("Gene.name", "Omega_BUSTED", "PosSel_BUSTED", "PValue_BUSTED")
-tab<-merge(tab, tmp, by="Gene.name")
-
-tmp<-dginn[dginn$Method=="MEME",c("Gene", "NbSites", "PSS")]
-names(tmp)<-c("Gene.name", "NbSites_MEME", "PSS_MEME")
-tab<-merge(tab, tmp, by="Gene.name")
-
-@
-
-\subsection{Write new table}
-<<>>=
-write.table(tab,
- "COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20200506.txt",
- row.names=F, quote=F, sep="\t")
-@
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Comparisons Primates}
-
-\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results}
-
-\subsubsection{Omega}
-
-Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
-<<omegaM7M8>>=
-
-plot(tab$whole.gene.dN.dS.model.0, tab$Omega_PamlM7M8,
- xlab="Omega Young-primate", ylab="Omega DGINN-Young-primate")
-@
-Quels sont les 2 gènes qui s'écartent de la bissectrice?
-<<>>=
-tab[tab$whole.gene.dN.dS.model.0<0.2 & tab$Omega_PamlM7M8>0.4,c("Gene.name")]
-tab[tab$whole.gene.dN.dS.model.0<0.6 & tab$Omega_PamlM7M8>0.7,c("Gene.name")]
-
-@
-
-
-\subsubsection{pvalues pour M7M8}
-
-Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne "PValue" + ligne "PamlM7M8", pour la sortie de dginn.
-
-<<pvalM7M8>>=
-
-plot(tab$pVal.M8vsM7, tab$PValue_PamlM7M8, pch=20,
- xlab="p-value Young-primate", ylab="p-value DGINN-Young-primate", main="M7vM8 Paml")
-points(tab$pVal.M8vsM7[tab$pVal.M8vsM7>0.05 & tab$PValue_PamlM7M8<0.05],
- tab$PValue_PamlM7M8[tab$pVal.M8vsM7>0.05 & tab$PValue_PamlM7M8<0.05],
- col="red", pch=20)
-points(tab$pVal.M8vsM7[tab$pVal.M8vsM7<0.05 & tab$PValue_PamlM7M8>0.05],
- tab$PValue_PamlM7M8[tab$pVal.M8vsM7<0.05 & tab$PValue_PamlM7M8>0.05],
- col="green", pch=20)
-
-legend("topleft", c("<0.05 in DGINN-Young-primate PamlM7M8 but >0.05 in Young M8vsM7",
- "<0.05 in Young M8vsM7 but >0.05 in DGINN-Young-primate PamlM7M8"),
- pch=20, col=c("red", "green"))
-
-@
-
-Quels sont les gènes en couleur:
-
-<<>>=
-na.omit(tab[(tab$pVal.M8vsM7>0.05 & tab$PValue_PamlM7M8<0.05),
-c("Gene.name", "pVal.M8vsM7", "PValue_PamlM7M8", "whole.gene.dN.dS.model.0", "Omega_PamlM7M8")])
-
-na.omit(tab[(tab$pVal.M8vsM7<0.05 & tab$PValue_PamlM7M8>0.05),
-c("Gene.name", "pVal.M8vsM7", "PValue_PamlM7M8", "whole.gene.dN.dS.model.0", "Omega_PamlM7M8")])
-@
-
-Focus sur le gène CIT pour lequel la différence est vraiment assez importante:
-
-<<cit>>=
-dginn[dginn$Gene=="CIT",]
-
-tab[tab$Gene.name=="CIT",1:20]
-@
-
-
-
-\subsubsection{Concordance des méthodes}
-
-Est-ce que les gènes avec une faible p-value sont détecté par 1,2,3,4 ou 5 méthodes en général?
-
-<<stripchart>>=
-nontab<-tab[tab$pVal.M8vsM7>=0.05,c("Gene.name","PosSel_PamlM1M2", "PosSel_PamlM7M8","PosSel_BppM1M2",
-"PosSel_BppM7M8", "PosSel_BUSTED")]
-
-
-non<-apply(nontab, 1, function(x) sum(x=="Y"))
-
-
-ouitab<-tab[tab$pVal.M8vsM7<0.05,c("Gene.name","PosSel_PamlM1M2", "PosSel_PamlM7M8","PosSel_BppM1M2",
-"PosSel_BppM7M8", "PosSel_BUSTED")]
-
-oui<-apply(ouitab, 1, function(x) sum(x=="Y"))
-
-stripchart(x=list(oui, non), method="jitter", jitter=0.2,
- vertical=T, pch=20, cex=0.5,
- group.names=c("Yes Young", "No Young"),
- ylab="Nb YES from dginn")
-
-
-@
-
-\subsection{Résultats Cooper-primate VS Young-primate}
-
-\subsubsection{How many genes in the Cooper-primate columns?}
-
-<<>>=
-# Temporary table with necessary columns
-
-tmp<-tab[,c("Gene.name", "whole.gene.dN.dS.model.0", "pVal.M8vsM7",
-"cooper.primates.Gene", "cooper.primates.Average_dNdS",
-"cooper.primates.M7.M8_p_value")]
-dim(tmp)
-
-# Lines with values in the cooper Gene names column
-dim(tmp[tmp$cooper.primates.Gene!="",])
-
-# Line with values (no NA) in the Cooper dNdS column
-sum(is.na(tmp$cooper.primates.Average_dNdS)==F)
-
-# Line with values (no NA) in the Cooper pvalue column
-sum(is.na(tmp$cooper.primates.M7.M8_p_value)==F)
-@
-
-\subsubsection{Omega}
-
-Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "cooper.primates.Average\_dNdS"
-
-<<omegaM7M8coop>>=
-plot(tab$whole.gene.dN.dS.model.0, tab$cooper.primates.Average_dNdS,
- xlab="Omega Young-primate", ylab="Omega Cooper-primate")
-@
-
-\subsubsection{pvalues pour M7M8}
-
-Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne cooper.primates.M7.M8\_p\_value (p-value de l'analyse de Cooper).
-
-<<pvalM7M8coop>>=
-
-plot(tab$pVal.M8vsM7, tab$cooper.primates.M7.M8_p_value, pch=20,
- xlab="p-value Young", ylab="p-value Cooper-primate", main="M7vM8 Paml-primate")
-
-points(tab$pVal.M8vsM7[tab$pVal.M8vsM7>0.05 & tab$cooper.primates.M7.M8_p_value<0.05],
- tab$cooper.primates.M7.M8_p_value[tab$pVal.M8vsM7>0.05 & tab$cooper.primates.M7.M8_p_value<0.05],
- col="red", pch=20)
-points(tab$pVal.M8vsM7[tab$pVal.M8vsM7<0.05 & tab$cooper.primates.M7.M8_p_value>0.05],
- tab$cooper.primates.M7.M8_p_value[tab$pVal.M8vsM7<0.05 & tab$cooper.primates.M7.M8_p_value>0.05],
- col="green", pch=20)
-
-legend("topleft", c("<0.05 in Cooper PamlM7M8 but >0.05 in Young M8vsM7",
- "<0.05 in Young M8vsM7 but >0.05 in Cooper PamlM7M8"),
- pch=20, col=c("red", "green"))
-
-@
-
-\subsection{Résultats DGINN sur alignement de Janet-Young (DGINN-Young-primate) VS Cooper-primates}
-
-\subsubsection{Omega}
-
-Comparaison des Omega: colonne colonne "cooper.primates.Average\_dNdS" VS omega de DGINN.
-
-<<omegaM7M8comp3>>=
-plot(tab$Omega_PamlM7M8, tab$cooper.primates.Average_dNdS,
- xlab="Omega DGINN-Young-primate", ylab="Omega Cooper-primate")
-@
-
-\subsubsection{pvalues pour M7M8}
-
-Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne "PValue" + ligne "PamlM7M8", pour la sortie de dginn.
-
-<<pvalM7M8comp3>>=
-
-plot(tab$PValue_PamlM7M8, tab$cooper.primates.M7.M8_p_value, pch=20,
- xlab="p-value DGINN-Young-primate", ylab="p-value Cooper-primate", main="M7vM8 Paml")
-
-points(tab$PValue_PamlM7M8[tab$PValue_PamlM7M8>0.05 & tab$cooper.primates.M7.M8_p_value<0.05],
- tab$cooper.primates.M7.M8_p_value[tab$PValue_PamlM7M8>0.05 & tab$cooper.primates.M7.M8_p_value<0.05],
- col="red", pch=20)
-points(tab$PValue_PamlM7M8[tab$PValue_PamlM7M8<0.05 & tab$cooper.primates.M7.M8_p_value>0.05],
- tab$cooper.primates.M7.M8_p_value[tab$PValue_PamlM7M8<0.05 & tab$cooper.primates.M7.M8_p_value>0.05],
- col="green", pch=20)
-
-legend("topleft", c("<0.05 in Cooper-primate PamlM7M8 but >0.05 in DGINN-Young-primate M8vsM7",
- "<0.05 in DGINN-Young-primate M8vsM7 but >0.05 in Cooper-primate PamlM7M8"),
- pch=20, col=c("red", "green"))
-
-@
-
-\subsection{Overlap}
-
-I will draw a venn diagramm for the positive genes in the 3 analyses.
-
-\subsubsection{Library and subtable}
-
-<<sub>>=
-library(VennDiagram)
-
-# keeps only genes analysed in all 3 experiments
-tmp<-na.omit(tab[,c("Gene.name", "pVal.M8vsM7", "cooper.primates.M7.M8_p_value",
- "PosSel_PamlM7M8", "PValue_PamlM7M8")])
-dim(tmp)
-@
-
-Il reste 186 gènes
-
-<<vennprimate>>=
-area1dginn<-sum(tmp$PosSel_PamlM7M8=="Y")
-area2jean<-sum(tmp$pVal.M8vsM7<0.05)
-area3coop<-sum(tmp$cooper.primates.M7.M8_p_val<0.05, na.rm=T)
-
-
-n12<-sum(tmp$PosSel_PamlM7M8=="Y" & tmp$pVal.M8vsM7<0.05)
-n23<-sum(tmp$pVal.M8vsM7<0.05 & tmp$cooper.primates.M7.M8_p_val<0.05, na.rm=T)
-n13<-sum(tmp$PosSel_PamlM7M8=="Y" & tmp$cooper.primates.M7.M8_p_val<0.05, na.rm=T)
-
-n123<-sum(tmp$PosSel_PamlM7M8=="Y" & tmp$pVal.M8vsM7<0.05 &
-tmp$cooper.primates.M7.M8_p_val<0.05, na.rm=T)
-
-draw.triple.venn(area1dginn, area2jean, area3coop,
-n12, n23, n13, n123,
-category=c("DGINN-Young-primate", "Young-primate", "Cooper-primate"))
-@
-
-\subsection{Mondrian}
-
-<<mondrianprimates>>=
-
-library(Mondrian)
-
-monddata<-as.data.frame(tmp$Gene.name)
-monddata$primates_dginn_young<-ifelse(tmp$PosSel_PamlM7M8=="Y", 1,0)
-monddata$primates_young<-ifelse(tmp$pVal.M8vsM7<0.05, 1, 0)
-monddata$primates_cooper<-ifelse(tmp$cooper.primates.M7.M8_p_val<0.05, 1, 0)
-
-mondrian(monddata[,2:4])
-@
-
-
-%\subsection{Comparaison des codons?}
-
-%Subtable with lines with both methods showing positive selection.
-
-<<eval=FALSE, echo=FALSE>>=
-%<<selec>>=
-#cas ou selection + dans les 2 cas
-sel<-na.omit(tab[(tab$pVal.M8vsM7<0.05 & tab$PValue_PamlM7M8<0.05),c("Gene.name", "pVal.M8vsM7", "PValue_PamlM7M8", "whole.gene.dN.dS.model.0", "Omega_PamlM7M8", "Number.of.codons.with.BEB....0.9", "Codons.under.positive.selection..BEB..0.9...alignment.position.", "NbSites_PamlM7M8","PSS_PamlM7M8")])
-
-dim(sel)
-head(sel)
-@
-
-<<nsites, eval=FALSE, echo=FALSE>>=
-%<<nsites>>=
-plot(sel$Number.of.codons.with.BEB....0.9, sel$NbSites_PamlM7M8)
-# toujours plus de codon dans la version de janet Young
-
-listdginn<-sapply(sel$PSS_PamlM7M8, function(x){
- tmp<-strsplit(as.character(x), split=",")[[1]]
- names(tmp)<-rep("dginn", length(tmp))
- return(tmp)
-})
-names(listdginn)<-sel$Gene.name
-
-
-
-listjanet<-sapply(sel$Codons.under.positive.selection..BEB..0.9...alignment.position., function(x){
-
- tmp<-strsplit(as.character(x), split=",")[[1]]
- tmp2<-sapply(tmp, function(x) strsplit(as.character(x), split="_")[[1]][1])
- tmp2<-unlist(tmp2)
- names(tmp2)<-rep("young", length(tmp2))
- return(unlist(tmp2))
-})
-
-names(listjanet)<-sel$Gene.name
-
-listjoined<-mapply(c, listdginn, listjanet, SIMPLIFY=FALSE)
-
-@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\section{Bats Comparisons}
-
-\subsection{Add DGINN results for Bats}
-
-Lecture du tableau.
-
-<<readtab4test, eval=F>>=
-# Tableau tel qu'il est à cet étape du script, pour travailler sur l'ajout du nouveau tableau bats sans recommencer au début à chaque fois.
-tab<-read.delim("COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20200506.txt",
- header=TRUE, sep="\t")
-@
-
-<<>>=
-#dginnbatsold<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/2020_bats_completeResults.csv",
-# fill=T, h=T)
-
-
-dginnbats<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/DGINN_202005281339summary_cleaned.tab",
- fill=T, h=T)
-
-
-dim(dginnbats)
-names(dginnbats)
-length(unique(dginnbats$Gene))
-length(unique(tab$cooper.batsGene))
-table(unique(tab$cooper.batsGene) %in% unique(dginnbats$Gene))
-@
-
-Which genes in the Cooper table are not in the gene output?
-
-<<>>=
-unique(tab$cooper.batsGene)[unique(tab$cooper.batsGene) %in% unique(dginnbats$Gene)==F]
-@
-
-Merge tables:
-
-<<bats>>=
-
-names(dginnbats)<-c("File", "bats_Name", "cooper.batsGene", paste0("bats_", names(dginnbats)[-(1:3)]))
-
-tab<-merge(tab,dginnbats, by="cooper.batsGene", all.x=T)
-@
-
-
-\subsection{Cooper-bats results vs DGINN-bats results}
-
-\subsubsection{Omega}
-
-<<omegaM7M8bats>>=
-
-plot(tab$cooper.batsAverage_dNdS, tab$bats_omegaM0codeml,
- xlab="Omega Cooper-bats", ylab="Omega DGINN-bats")
-@
-
-\subsubsection{pvalues pour M7M8}
-
-<<pvalM7M8bats>>=
-tab$bats_codemlM7M8.p.value<-as.numeric(as.character(tab$bats_codemlM7M8.p.value))
-
-plot(tab$cooper.batsM7.M8_p_value, tab$bats_codemlM7M8.p.value, pch=20,
- xlab="p-value Cooper-bats", ylab="p-value DGINN-bats", main="M7vM8 Paml")
-
-points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_codemlM7M8.p.value<0.05],
- tab$bats_codemlM7M8.p.value[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_codemlM7M8.p.value<0.05],
- col="red", pch=20)
-points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_codemlM7M8.p.value>0.05],
- tab$bats_codemlM7M8.p.value[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_codemlM7M8.p.value>0.05],
- col="green", pch=20)
-
-
-legend("topleft", c("<0.05 in DGINN-bats but >0.05 in Cooper-bats",
- "<0.05 in Cooper-bats but >0.05 in DGINN-bats"),
- pch=20, col=c("red", "green"))
-
-@
-
-
-
-
-\subsection{Comparaison Cooper-Hawkins}
-
-
-\subsubsection{pvalues pour M7M8}
-
-<<pvalM7M8comp2>>=
-
-plot(tab$cooper.batsM7.M8_p_value, tab$hawkins_Positive.Selection..M8vM8a.p.value,
- pch=20, xlab="p-value Cooper-bats", ylab="p-value hawkins-bats", main="M7vM8 Paml")
-
-points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value>0.05 &
- tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05],
- tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$cooper.batsM7.M8_p_value>0.05 &
- tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05],
- col="red", pch=20)
-points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value<0.05 &
- tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05],
- tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$cooper.batsM7.M8_p_value<0.05 &
- tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05],
- col="green", pch=20)
-
-
-legend("topleft", c("<0.05 in Hawkins but >0.05 in Cooper",
- "<0.05 in Cooper but >0.05 in Hawkins"),
- pch=20, col=c("red", "green"))
-
-@
-
-
-\subsection{Comparaison dginn-Hawkins}
-
-<<pvalM7M8compautre>>=
-
-plot(tab$hawkins_Positive.Selection..M8vM8a.p.value, tab$bats_codemlM7M8.p.value,
- pch=20, xlab="p-value hawkins-bats", ylab="p-value DGINN-bats", main="M7vM8 Paml")
-
-points(tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05 &
- tab$bats_codemlM7M8.p.value<0.05],
- tab$bats_codemlM7M8.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05 &
- tab$bats_codemlM7M8.p.value<0.05], col="red", pch=20)
-points(tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05 &
- tab$bats_codemlM7M8.p.value>0.05],
- tab$bats_codemlM7M8.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05 &
- tab$bats_codemlM7M8.p.value>0.05], col="green", pch=20)
-
-
-legend("topleft", c("<0.05 in DGINN-bats but >0.05 in Hawkins",
- "<0.05 in Hawkinsbut >0.05 in DGINN-bats"),
- pch=20, col=c("red", "green"))
-
-@
-
-
-
-
-
-\subsection{Diagramme de Venn}
-
-I will draw a venn diagramm for the positive genes in the 3 analyses.
-
-\subsubsection{subtab}
-
-<<subbats>>=
-tmp<-na.omit(tab[,c("Gene.name", "bats_codemlM7M8.p.value", "hawkins_Positive.Selection..M8vM8a.p.value", "cooper.batsM7.M8_p_value")])
-dim(tmp)
-@
-
-154 genes (present in the 3 experiments)
-
-\subsubsection{figure}
-<<vennbats>>=
-area1dginn<-sum(tmp$bats_codemlM7M8.p.value<0.05, na.rm=T)
-area2hawk<-sum(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, na.rm=T)
-area3coop<-sum(tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
-
-
-n12<-sum(tmp$bats_codemlM7M8.p.value<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, na.rm=T)
-
-n23<-sum(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
-
-n13<-sum(tmp$bats_codemlM7M8.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
-
-
-n123<-sum(tmp$bats_codemlM7M8.p.value<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
-
-draw.triple.venn(area1dginn, area2hawk, area3coop,
-n12, n23, n13, n123,
-category=c("DGINN-Young-bats", "Hawkins-bats", "Cooper-bats"))
-
-
-@
-
-\subsection{Mondrian}
-
-<<mondrianbats>>=
-library(Mondrian)
-
-monddata<-as.data.frame(tmp$Gene.name)
-monddata$bats_dginn<-ifelse(tmp$bats_codemlM7M8.p.value<0.05, 1,0)
-monddata$bats_hawkins<-ifelse(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, 1, 0)
-monddata$bats_cooper<-ifelse(tmp$cooper.batsM7.M8_p_value<0.05, 1, 0)
-
-mondrian(monddata[,2:4])
-@
-
-\section{To do}
-
-Comparaison G4 pas G4
-
-\end{document}
-
diff --git a/covid_comp.pdf b/covid_comp.pdf
deleted file mode 100644
index e14d50ff9a0afb4c455f56c31d9313b987382db0..0000000000000000000000000000000000000000
Binary files a/covid_comp.pdf and /dev/null differ
diff --git a/covid_comp.tex b/covid_comp.tex
deleted file mode 100644
index 1965f848b2bbb5177a80f8b362350f670b4f7e69..0000000000000000000000000000000000000000
--- a/covid_comp.tex
+++ /dev/null
@@ -1,1053 +0,0 @@
-\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{Mai 2020} % Activate to display a given date or no date
-\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
-\begin{document}
-\maketitle
-
-\tableofcontents
-
-\newpage
-
-\section{Files manipulations}
-
-I will compare Janet Young's results to DGINN results, on the SAME alignment.
-
-\subsection{Read Janet Young's table}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"}\hlstd{,}
- \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{dec}\hlstd{=}\hlstr{","}\hlstd{)}
-\hlkwd{dim}\hlstd{(tab)}
-\end{alltt}
-\begin{verbatim}
-## [1] 332 84
-\end{verbatim}
-\begin{alltt}
-\hlkwd{names}\hlstd{(tab)}
-\end{alltt}
-\begin{verbatim}
-## [1] "PreyGene"
-## [2] "PreyGene_JYname"
-## [3] "BaitShort"
-## [4] "Gene.name"
-## [5] "list"
-## [6] "description"
-## [7] "other.names"
-## [8] "top40_posSeln"
-## [9] "Num.primate.seqs"
-## [10] "Alignment.length..nucleotides."
-## [11] "Alignment.length..codons."
-## [12] "whole.gene.dN.dS.model.0"
-## [13] "total.tree.length"
-## [14] "total.dN.tree.length"
-## [15] "total.dS.tree.length"
-## [16] "p.value.M8vsM8a..raw."
-## [17] "p.value.M8vsM8a..BH.corrected."
-## [18] "pVal.M8vsM7"
-## [19] "pVal.M8vsM7.adj"
-## [20] "pVal.M2vsM1"
-## [21] "pVal.M2vsM1.adj"
-## [22] "X..codons.under.positive.selection"
-## [23] "dN.dS.of.positively.selected.codons"
-## [24] "Number.of.codons.with.BEB....0.9"
-## [25] "Codons.under.positive.selection..BEB..0.9...alignment.position."
-## [26] "cooper.batsGene"
-## [27] "cooper.batsGene_Ensembl_ID"
-## [28] "cooper.batsIsoform_Ensembl_ID"
-## [29] "cooper.batsSpecies"
-## [30] "cooper.batsReference_length.aa."
-## [31] "cooper.batsPercent_analyzed"
-## [32] "cooper.batsAverage_dNdS"
-## [33] "cooper.batsMaximum_dS"
-## [34] "cooper.batsAverage_M7_tree"
-## [35] "cooper.batsAverage_M8_tree"
-## [36] "cooper.batsM7_log_likelihood"
-## [37] "cooper.batsM8_log_likelihood"
-## [38] "cooper.batsM7.M8_p_value"
-## [39] "cooper.batsM8a_log_likelihood"
-## [40] "cooper.batsM8.M8a_pvalue"
-## [41] "cooper.batsBEB_hits.pp.0.95."
-## [42] "cooper.batsBEB_sites"
-## [43] "cooper.primates.Gene"
-## [44] "cooper.primates.Gene_Ensembl_ID"
-## [45] "cooper.primates.Isoform_Ensembl_ID"
-## [46] "cooper.primates.Species"
-## [47] "cooper.primates.Reference_length.aa."
-## [48] "cooper.primates.Percent_analyzed"
-## [49] "cooper.primates.Average_dNdS"
-## [50] "cooper.primates.Maximum_dS"
-## [51] "cooper.primates.Average_M7_tree"
-## [52] "cooper.primates.Average_M8_tree"
-## [53] "cooper.primates.M7_log_likelihood"
-## [54] "cooper.primates.M8_log_likelihood"
-## [55] "cooper.primates.M7.M8_p_value"
-## [56] "cooper.primates.M8a_log_likelihood"
-## [57] "cooper.primates.M8.M8a_pvalue"
-## [58] "cooper.primates.BEB_hits.pp.0.95."
-## [59] "cooper.primates.BEB_sites"
-## [60] "hawkins_Gene"
-## [61] "hawkins_Positive.Selection..M8vM8a.p.value"
-## [62] "hawkins_Positive.Selection..M8vM8a.FDR.corrected.p.value"
-## [63] "hawkins_Gene.Name.Alias"
-## [64] "hawkins_Connection.to.immunity.or.pathogens"
-## [65] "hawkins_Connection.to.reproduction"
-## [66] "hawkins_Connection.to.collagen"
-## [67] "hawkins_Connection.to.peroxisome"
-## [68] "hawkins_Gene.Description.for.Human.Ortholog..from.Genbank.GENE.database."
-## [69] "CpGmask.numNT"
-## [70] "CpGmask.numAA"
-## [71] "CpGmask.overall.dN.dS"
-## [72] "CpGmask.total.tree.length"
-## [73] "CpGmask.total.dN.tree.length"
-## [74] "CpGmask.total.dS.tree.length"
-## [75] "CpGmask.pVal.M8vsM8a"
-## [76] "CpGmask.pVal.M8vsM8a.adj"
-## [77] "CpGmask.pVal.M8vsM7"
-## [78] "CpGmask.pVal.M8vsM7.adj"
-## [79] "CpGmask.pVal.M2vsM1"
-## [80] "CpGmask.pVal.M2vsM1.adj"
-## [81] "CpGmask.percent.sites.under.positive.selection"
-## [82] "CpGmask.dN.dS.of.selected.sites"
-## [83] "CpGmask.num.sites.with.BEB...0.9"
-## [84] "CpGmask.which.sites.have.BEB...0.9"
-\end{verbatim}
-\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{dginn}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/summary.res"}\hlstd{,}
- \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
-
-\hlkwd{dim}\hlstd{(dginn)}
-\end{alltt}
-\begin{verbatim}
-## [1] 1992 7
-\end{verbatim}
-\begin{alltt}
-\hlkwd{names}\hlstd{(dginn)}
-\end{alltt}
-\begin{verbatim}
-## [1] "Gene" "Omega" "Method" "PosSel" "PValue" "NbSites" "PSS"
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-\subsection{Joining table}
-
-\subsubsection{Based on which column?}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{head}\hlstd{(tab)[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{]}
-\end{alltt}
-\begin{verbatim}
-## PreyGene PreyGene_JYname BaitShort Gene.name list
-## 1 PCNT PCNT nsp13 PCNT list26_COV_list4dataset2nonOrf
-## 2 PVR PVR orf8 PVR list23_COV_list1orf
-## 3 POLA1 POLA1 nsp1 POLA1 list24_COV_list2nonOrf
-## 4 FASTKD5 FASTKD5 M FASTKD5 list26_COV_list4dataset2nonOrf
-## 5 PRIM2 PRIM2 nsp1 PRIM2 list24_COV_list2nonOrf
-## 6 ITGB1 ITGB1 orf8 ITGB1 list25_COV_list3dataset2orf
-\end{verbatim}
-\begin{alltt}
-\hlcom{# gene avec un nom bizar dans certaines colomne}
-\hlstd{tab[}\hlnum{158}\hlstd{,}\hlnum{1}\hlopt{:}\hlnum{10}\hlstd{]}
-\end{alltt}
-\begin{verbatim}
-## PreyGene PreyGene_JYname BaitShort Gene.name list
-## 158 MTARC1 01/03/2020 nsp7 01/03/2020 list24_COV_list2nonOrf
-## description other.names top40_posSeln
-## 158 mitochondrial amidoxime reducing component 1 MOSC1 no
-## Num.primate.seqs Alignment.length..nucleotides.
-## 158 24 1023
-\end{verbatim}
-\begin{alltt}
-\hlcom{#}
-\hlkwd{length}\hlstd{(}\hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene))}
-\end{alltt}
-\begin{verbatim}
-## [1] 332
-\end{verbatim}
-\begin{alltt}
-\hlkwd{length}\hlstd{(}\hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{PreyGene))}
-\end{alltt}
-\begin{verbatim}
-## [1] 332
-\end{verbatim}
-\begin{alltt}
-\hlkwd{length}\hlstd{(}\hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name))}
-\end{alltt}
-\begin{verbatim}
-## [1] 332
-\end{verbatim}
-\begin{alltt}
-\hlcom{#quelle paire de colonne contient le plus de noms identiques}
-\hlkwd{sum}\hlstd{(}\hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene)} \hlopt{%in%} \hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{PreyGene))}
-\end{alltt}
-\begin{verbatim}
-## [1] 314
-\end{verbatim}
-\begin{alltt}
-\hlkwd{sum}\hlstd{(}\hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene)} \hlopt{%in%} \hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name))}
-\end{alltt}
-\begin{verbatim}
-## [1] 331
-\end{verbatim}
-\begin{alltt}
-\hlcom{# dginn$Gene et tab$Gene.name presque identiques sauf 1 ligne. }
-\hlcom{# Je soupçonne que c'est celle là :}
-\hlstd{tab[}\hlnum{158}\hlstd{,}\hlnum{1}\hlopt{:}\hlnum{10}\hlstd{]}
-\end{alltt}
-\begin{verbatim}
-## PreyGene PreyGene_JYname BaitShort Gene.name list
-## 158 MTARC1 01/03/2020 nsp7 01/03/2020 list24_COV_list2nonOrf
-## description other.names top40_posSeln
-## 158 mitochondrial amidoxime reducing component 1 MOSC1 no
-## Num.primate.seqs Alignment.length..nucleotides.
-## 158 24 1023
-\end{verbatim}
-\begin{alltt}
-\hlcom{# Verif:}
-\hlstd{tab[,}\hlnum{1}\hlopt{:}\hlnum{10}\hlstd{][(tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene))}\hlopt{==}\hlstd{F,]}
-\end{alltt}
-\begin{verbatim}
-## PreyGene PreyGene_JYname BaitShort Gene.name list
-## 158 MTARC1 01/03/2020 nsp7 01/03/2020 list24_COV_list2nonOrf
-## description other.names top40_posSeln
-## 158 mitochondrial amidoxime reducing component 1 MOSC1 no
-## Num.primate.seqs Alignment.length..nucleotides.
-## 158 24 1023
-\end{verbatim}
-\begin{alltt}
-\hlcom{# yep}
-
-\hlcom{# Remplacement manuel par}
-\hlkwd{as.character}\hlstd{(}\hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene)[(}\hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene)} \hlopt{%in%} \hlstd{tab}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlstd{F])}
-\end{alltt}
-\begin{verbatim}
-## [1] "MARC1"
-\end{verbatim}
-\begin{alltt}
-\hlcom{# dans le tableau de Janet}
-
-\hlstd{val_remp}\hlkwb{=}\hlkwd{as.character}\hlstd{(}\hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene)[(}\hlkwd{unique}\hlstd{(dginn}\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{$}\hlstd{Gene.name[}\hlnum{158}\hlstd{]}\hlkwb{<-}\hlstd{val_remp}
-
-\hlkwd{sum}\hlstd{(}\hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene)} \hlopt{%in%} \hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name))}
-\end{alltt}
-\begin{verbatim}
-## [1] 332
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-\subsubsection{New columns}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{add_col}\hlkwb{<-}\hlkwa{function}\hlstd{(}\hlkwc{method}\hlstd{=}\hlstr{"PamlM1M2"}\hlstd{)\{}
-
-\hlstd{tmp}\hlkwb{<-}\hlstd{dginn[dginn}\hlopt{$}\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{dginn[dginn}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{"BUSTED"}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"Omega"}\hlstd{,} \hlstr{"PosSel"}\hlstd{,} \hlstr{"PValue"}\hlstd{)]}
-\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"Omega_BUSTED"}\hlstd{,} \hlstr{"PosSel_BUSTED"}\hlstd{,} \hlstr{"PValue_BUSTED"}\hlstd{)}
-\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
-
-\hlstd{tmp}\hlkwb{<-}\hlstd{dginn[dginn}\hlopt{$}\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{Write 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_PAMLresults_332hits_plusBatScreens_plusDGINN_20200506.txt"}\hlstd{,}
- \hlkwc{row.names}\hlstd{=F,} \hlkwc{quote}\hlstd{=F,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Comparisons Primates}
-
-\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results}
-
-\subsubsection{Omega}
-
-Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\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{)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/omegaM7M8-1}
-
-\end{knitrout}
-Quels sont les 2 gènes qui s'écartent de la bissectrice?
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.2} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{>}\hlnum{0.4}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{)]}
-\end{alltt}
-\begin{verbatim}
-## [1] "MRPS2"
-\end{verbatim}
-\begin{alltt}
-\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.6} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{>}\hlnum{0.7}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{)]}
-\end{alltt}
-\begin{verbatim}
-## [1] "PVR"
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-
-\subsubsection{pvalues pour M7M8}
-
-Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne "PValue" + ligne "PamlM7M8", pour la sortie de dginn.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7, tab}\hlopt{$}\hlstd{PValue_PamlM7M8,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"p-value Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value DGINN-Young-primate"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-
-\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in DGINN-Young-primate PamlM7M8 but >0.05 in Young M8vsM7"}\hlstd{,}
- \hlstr{"<0.05 in Young M8vsM7 but >0.05 in DGINN-Young-primate PamlM7M8"}\hlstd{),}
- \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/pvalM7M8-1}
-
-\end{knitrout}
-
-Quels sont les gènes en couleur:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{na.omit}\hlstd{(tab[(tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{),}
-\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"pVal.M8vsM7"}\hlstd{,} \hlstr{"PValue_PamlM7M8"}\hlstd{,} \hlstr{"whole.gene.dN.dS.model.0"}\hlstd{,} \hlstr{"Omega_PamlM7M8"}\hlstd{)])}
-\end{alltt}
-\begin{verbatim}
-## Gene.name pVal.M8vsM7 PValue_PamlM7M8 whole.gene.dN.dS.model.0
-## 51 CIT 0.103170 1.854024e-02 0.03889
-## 101 FBN2 0.174750 2.253070e-08 0.06871
-## 158 MARK1 0.062265 1.890420e-02 0.08147
-## 196 NUP88 0.052061 4.950260e-02 0.19123
-## 316 UBXN8 0.053229 3.945009e-02 0.50084
-## 322 VPS11 0.108710 3.061568e-02 0.04236
-## Omega_PamlM7M8
-## 51 0.04325399
-## 101 0.07233605
-## 158 0.08802245
-## 196 0.20601208
-## 316 0.50718198
-## 322 0.04780560
-\end{verbatim}
-\begin{alltt}
-\hlkwd{na.omit}\hlstd{(tab[(tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{),}
-\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"pVal.M8vsM7"}\hlstd{,} \hlstr{"PValue_PamlM7M8"}\hlstd{,} \hlstr{"whole.gene.dN.dS.model.0"}\hlstd{,} \hlstr{"Omega_PamlM7M8"}\hlstd{)])}
-\end{alltt}
-\begin{verbatim}
-## Gene.name pVal.M8vsM7 PValue_PamlM7M8 whole.gene.dN.dS.model.0
-## 68 DCTPP1 0.0431830 0.10613016 0.29992
-## 181 NDUFB9 0.0024264 0.05119297 0.29487
-## 188 NLRX1 0.0463220 0.13614538 0.17885
-## 197 NUP98 0.0345210 0.98219934 0.17017
-## 284 STOM 0.0345710 0.19872467 0.16126
-## Omega_PamlM7M8
-## 68 0.3538646
-## 181 0.3104234
-## 188 0.2159544
-## 197 0.1772109
-## 284 0.1477986
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-Focus sur le gène CIT pour lequel la différence est vraiment assez importante:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{dginn[dginn}\hlopt{$}\hlstd{Gene}\hlopt{==}\hlstr{"CIT"}\hlstd{,]}
-\end{alltt}
-\begin{verbatim}
-## Gene Omega Method PosSel PValue NbSites
-## 1201 CIT 0.04325399 BUSTED N 1.000000e+00 NA
-## 1202 CIT 0.04325399 BppM1M2 N 9.999983e-01 NA
-## 1203 CIT 0.04325399 BppM7M8 Y 2.254251e-05 11
-## 1204 CIT 0.04325399 PamlM1M2 N 1.000000e+00 NA
-## 1205 CIT 0.04325399 PamlM7M8 Y 1.854024e-02 0
-## 1206 CIT 0.04325399 MEME NA 1
-## PSS
-## 1201
-## 1202
-## 1203 258, 8, 1835, 304, 369, 338, 434, 625, 151, 410, 255
-## 1204
-## 1205
-## 1206 410
-\end{verbatim}
-\begin{alltt}
-\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"CIT"}\hlstd{,}\hlnum{1}\hlopt{:}\hlnum{20}\hlstd{]}
-\end{alltt}
-\begin{verbatim}
-## Gene.name PreyGene PreyGene_JYname BaitShort list
-## 51 CIT CIT CIT nsp13 list26_COV_list4dataset2nonOrf
-## description other.names
-## 51 citron rho-interacting serine/threonine kinase CITK|CRIK|MCPH17|STK21
-## top40_posSeln Num.primate.seqs Alignment.length..nucleotides.
-## 51 no 24 6210
-## Alignment.length..codons. whole.gene.dN.dS.model.0 total.tree.length
-## 51 2070 0.03889 0.33654
-## total.dN.tree.length total.dS.tree.length p.value.M8vsM8a..raw.
-## 51 0.014 0.3603 0.99887
-## p.value.M8vsM8a..BH.corrected. pVal.M8vsM7 pVal.M8vsM7.adj pVal.M2vsM1
-## 51 1 0.10317 0.3747212 1
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-
-
-\subsubsection{Concordance des méthodes}
-
-Est-ce que les gènes avec une faible p-value sont détecté par 1,2,3,4 ou 5 méthodes en général?
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{nontab}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>=}\hlnum{0.05}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,}\hlstr{"PosSel_PamlM1M2"}\hlstd{,} \hlstr{"PosSel_PamlM7M8"}\hlstd{,}\hlstr{"PosSel_BppM1M2"}\hlstd{,}
-\hlstr{"PosSel_BppM7M8"}\hlstd{,} \hlstr{"PosSel_BUSTED"}\hlstd{)]}
-
-
-\hlstd{non}\hlkwb{<-}\hlkwd{apply}\hlstd{(nontab,} \hlnum{1}\hlstd{,} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{sum}\hlstd{(x}\hlopt{==}\hlstr{"Y"}\hlstd{))}
-
-
-\hlstd{ouitab}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,}\hlstr{"PosSel_PamlM1M2"}\hlstd{,} \hlstr{"PosSel_PamlM7M8"}\hlstd{,}\hlstr{"PosSel_BppM1M2"}\hlstd{,}
-\hlstr{"PosSel_BppM7M8"}\hlstd{,} \hlstr{"PosSel_BUSTED"}\hlstd{)]}
-
-\hlstd{oui}\hlkwb{<-}\hlkwd{apply}\hlstd{(ouitab,} \hlnum{1}\hlstd{,} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{sum}\hlstd{(x}\hlopt{==}\hlstr{"Y"}\hlstd{))}
-
-\hlkwd{stripchart}\hlstd{(}\hlkwc{x}\hlstd{=}\hlkwd{list}\hlstd{(oui, non),} \hlkwc{method}\hlstd{=}\hlstr{"jitter"}\hlstd{,} \hlkwc{jitter}\hlstd{=}\hlnum{0.2}\hlstd{,}
- \hlkwc{vertical}\hlstd{=T,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{,}
- \hlkwc{group.names}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Yes Young"}\hlstd{,} \hlstr{"No Young"}\hlstd{),}
- \hlkwc{ylab}\hlstd{=}\hlstr{"Nb YES from dginn"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/stripchart-1}
-
-\end{knitrout}
-
-\subsection{Résultats Cooper-primate VS Young-primate}
-
-\subsubsection{How many genes in the Cooper-primate columns?}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{# Temporary table with necessary columns}
-
-\hlstd{tmp}\hlkwb{<-}\hlstd{tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"whole.gene.dN.dS.model.0"}\hlstd{,} \hlstr{"pVal.M8vsM7"}\hlstd{,}
-\hlstr{"cooper.primates.Gene"}\hlstd{,} \hlstr{"cooper.primates.Average_dNdS"}\hlstd{,}
-\hlstr{"cooper.primates.M7.M8_p_value"}\hlstd{)]}
-\hlkwd{dim}\hlstd{(tmp)}
-\end{alltt}
-\begin{verbatim}
-## [1] 332 6
-\end{verbatim}
-\begin{alltt}
-\hlcom{# Lines with values in the cooper Gene names column}
-\hlkwd{dim}\hlstd{(tmp[tmp}\hlopt{$}\hlstd{cooper.primates.Gene}\hlopt{!=}\hlstr{""}\hlstd{,])}
-\end{alltt}
-\begin{verbatim}
-## [1] 207 6
-\end{verbatim}
-\begin{alltt}
-\hlcom{# Line with values (no NA) in the Cooper dNdS column}
-\hlkwd{sum}\hlstd{(}\hlkwd{is.na}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.primates.Average_dNdS)}\hlopt{==}\hlstd{F)}
-\end{alltt}
-\begin{verbatim}
-## [1] 201
-\end{verbatim}
-\begin{alltt}
-\hlcom{# Line with values (no NA) in the Cooper pvalue column}
-\hlkwd{sum}\hlstd{(}\hlkwd{is.na}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value)}\hlopt{==}\hlstd{F)}
-\end{alltt}
-\begin{verbatim}
-## [1] 207
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-\subsubsection{Omega}
-
-Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "cooper.primates.Average\_dNdS"
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0, tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega Cooper-primate"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/omegaM7M8coop-1}
-
-\end{knitrout}
-
-\subsubsection{pvalues pour M7M8}
-
-Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne cooper.primates.M7.M8\_p\_value (p-value de l'analyse de Cooper).
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7, tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"p-value Young"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value Cooper-primate"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml-primate"}\hlstd{)}
-
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-
-\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in Cooper PamlM7M8 but >0.05 in Young M8vsM7"}\hlstd{,}
- \hlstr{"<0.05 in Young M8vsM7 but >0.05 in Cooper PamlM7M8"}\hlstd{),}
- \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/pvalM7M8coop-1}
-
-\end{knitrout}
-
-\subsection{Résultats DGINN sur alignement de Janet-Young (DGINN-Young-primate) VS Cooper-primates}
-
-\subsubsection{Omega}
-
-Comparaison des Omega: colonne colonne "cooper.primates.Average\_dNdS" VS omega de DGINN.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{Omega_PamlM7M8, tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"Omega DGINN-Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega Cooper-primate"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/omegaM7M8comp3-1}
-
-\end{knitrout}
-
-\subsubsection{pvalues pour M7M8}
-
-Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne "PValue" + ligne "PamlM7M8", pour la sortie de dginn.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{PValue_PamlM7M8, tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"p-value DGINN-Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value Cooper-primate"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
-
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{PValue_PamlM7M8[tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value[tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{PValue_PamlM7M8[tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value[tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-
-\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in Cooper-primate PamlM7M8 but >0.05 in DGINN-Young-primate M8vsM7"}\hlstd{,}
- \hlstr{"<0.05 in DGINN-Young-primate M8vsM7 but >0.05 in Cooper-primate PamlM7M8"}\hlstd{),}
- \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/pvalM7M8comp3-1}
-
-\end{knitrout}
-
-\subsection{Overlap}
-
-I will draw a venn diagramm for the positive genes in the 3 analyses.
-
-\subsubsection{Library and subtable}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{library}\hlstd{(VennDiagram)}
-
-\hlcom{# keeps only genes analysed in all 3 experiments}
-\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"pVal.M8vsM7"}\hlstd{,} \hlstr{"cooper.primates.M7.M8_p_value"}\hlstd{,}
- \hlstr{"PosSel_PamlM7M8"}\hlstd{,} \hlstr{"PValue_PamlM7M8"}\hlstd{)])}
-\hlkwd{dim}\hlstd{(tmp)}
-\end{alltt}
-\begin{verbatim}
-## [1] 186 5
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-Il reste 186 gènes
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{area1dginn}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{)}
-\hlstd{area2jean}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{)}
-\hlstd{area3coop}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-
-
-\hlstd{n12}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{)}
-\hlstd{n23}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-\hlstd{n13}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-
-\hlstd{n123}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&}
-\hlstd{tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-
-\hlkwd{draw.triple.venn}\hlstd{(area1dginn, area2jean, area3coop,}
-\hlstd{n12, n23, n13, n123,}
-\hlkwc{category}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN-Young-primate"}\hlstd{,} \hlstr{"Young-primate"}\hlstd{,} \hlstr{"Cooper-primate"}\hlstd{))}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/vennprimate-1}
-\begin{kframe}\begin{verbatim}
-## (polygon[GRID.polygon.836], polygon[GRID.polygon.837], polygon[GRID.polygon.838], polygon[GRID.polygon.839], polygon[GRID.polygon.840], polygon[GRID.polygon.841], text[GRID.text.842], text[GRID.text.843], text[GRID.text.844], text[GRID.text.845], text[GRID.text.846], text[GRID.text.847], text[GRID.text.848], text[GRID.text.849], text[GRID.text.850], text[GRID.text.851])
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-\subsection{Mondrian}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{library}\hlstd{(Mondrian)}
-
-\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
-\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
-\hlstd{monddata}\hlopt{$}\hlstd{primates_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
-\hlstd{monddata}\hlopt{$}\hlstd{primates_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
-
-\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{])}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/mondrianprimates-1}
-
-\end{knitrout}
-
-
-%\subsection{Comparaison des codons?}
-
-%Subtable with lines with both methods showing positive selection.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\section{Bats Comparisons}
-
-\subsection{Add DGINN results for Bats}
-
-Lecture du tableau.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{# Tableau tel qu'il est à cet étape du script, pour travailler sur l'ajout du nouveau tableau bats sans recommencer au début à chaque fois.}
-\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlstr{"COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20200506.txt"}\hlstd{,}
- \hlkwc{header}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlcom{#dginnbatsold<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/2020_bats_completeResults.csv", }
-\hlcom{# fill=T, h=T)}
-
-
-\hlstd{dginnbats}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/DGINN_202005281339summary_cleaned.tab"}\hlstd{,}
- \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
-
-
-\hlkwd{dim}\hlstd{(dginnbats)}
-\end{alltt}
-\begin{verbatim}
-## [1] 349 27
-\end{verbatim}
-\begin{alltt}
-\hlkwd{names}\hlstd{(dginnbats)}
-\end{alltt}
-\begin{verbatim}
-## [1] "File" "Name" "Gene"
-## [4] "GeneSize" "NbSpecies" "omegaM0Bpp"
-## [7] "omegaM0codeml" "BUSTED" "BUSTED.p.value"
-## [10] "MEME.NbSites" "MEME.PSS" "BppM1M2"
-## [13] "BppM1M2.p.value" "BppM1M2.NbSites" "BppM1M2.PSS"
-## [16] "BppM7M8" "BppM7M8.p.value" "BppM7M8.NbSites"
-## [19] "BppM7M8.PSS" "codemlM1M2" "codemlM1M2.p.value"
-## [22] "codemlM1M2.NbSites" "codemlM1M2.PSS" "codemlM7M8"
-## [25] "codemlM7M8.p.value" "codemlM7M8.NbSites" "codemlM7M8.PSS"
-\end{verbatim}
-\begin{alltt}
-\hlkwd{length}\hlstd{(}\hlkwd{unique}\hlstd{(dginnbats}\hlopt{$}\hlstd{Gene))}
-\end{alltt}
-\begin{verbatim}
-## [1] 349
-\end{verbatim}
-\begin{alltt}
-\hlkwd{length}\hlstd{(}\hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsGene))}
-\end{alltt}
-\begin{verbatim}
-## [1] 218
-\end{verbatim}
-\begin{alltt}
-\hlkwd{table}\hlstd{(}\hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsGene)} \hlopt{%in%} \hlkwd{unique}\hlstd{(dginnbats}\hlopt{$}\hlstd{Gene))}
-\end{alltt}
-\begin{verbatim}
-##
-## FALSE TRUE
-## 3 215
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-Which genes in the Cooper table are not in the gene output?
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsGene)[}\hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsGene)} \hlopt{%in%} \hlkwd{unique}\hlstd{(dginnbats}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlstd{F]}
-\end{alltt}
-\begin{verbatim}
-## [1] BCS1L C1orf50
-## 218 Levels: AAR2 AASS AATF ACADM ACSL3 ADAMTS1 AGPS AKAP8L ALG11 ALG5 ... ZYG11B
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-Merge tables:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"bats_Name"}\hlstd{,} \hlstr{"cooper.batsGene"}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{"bats_"}\hlstd{,} \hlkwd{names}\hlstd{(dginnbats)[}\hlopt{-}\hlstd{(}\hlnum{1}\hlopt{:}\hlnum{3}\hlstd{)]))}
-
-\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnbats,} \hlkwc{by}\hlstd{=}\hlstr{"cooper.batsGene"}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-
-\subsection{Cooper-bats results vs DGINN-bats results}
-
-\subsubsection{Omega}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsAverage_dNdS, tab}\hlopt{$}\hlstd{bats_omegaM0codeml,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Cooper-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-bats"}\hlstd{)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/omegaM7M8bats-1}
-
-\end{knitrout}
-
-\subsubsection{pvalues pour M7M8}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value))}
-\end{alltt}
-
-
-{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value, tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"p-value Cooper-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value DGINN-bats"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
-
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-
-
-\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in DGINN-bats but >0.05 in Cooper-bats"}\hlstd{,}
- \hlstr{"<0.05 in Cooper-bats but >0.05 in DGINN-bats"}\hlstd{),}
- \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/pvalM7M8bats-1}
-
-\end{knitrout}
-
-
-
-
-\subsection{Comparaison Cooper-Hawkins}
-
-
-\subsubsection{pvalues pour M7M8}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value, tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value,}
- \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"p-value Cooper-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value hawkins-bats"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
-
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-
-
-\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in Hawkins but >0.05 in Cooper"}\hlstd{,}
- \hlstr{"<0.05 in Cooper but >0.05 in Hawkins"}\hlstd{),}
- \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/pvalM7M8comp2-1}
-
-\end{knitrout}
-
-
-\subsection{Comparaison dginn-Hawkins}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value, tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value,}
- \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"p-value hawkins-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value DGINN-bats"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
-
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{>}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{>}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],} \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-
-
-\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in DGINN-bats but >0.05 in Hawkins"}\hlstd{,}
- \hlstr{"<0.05 in Hawkinsbut >0.05 in DGINN-bats"}\hlstd{),}
- \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/pvalM7M8compautre-1}
-
-\end{knitrout}
-
-
-
-
-
-\subsection{Diagramme de Venn}
-
-I will draw a venn diagramm for the positive genes in the 3 analyses.
-
-\subsubsection{subtab}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_codemlM7M8.p.value"}\hlstd{,} \hlstr{"hawkins_Positive.Selection..M8vM8a.p.value"}\hlstd{,} \hlstr{"cooper.batsM7.M8_p_value"}\hlstd{)])}
-\hlkwd{dim}\hlstd{(tmp)}
-\end{alltt}
-\begin{verbatim}
-## [1] 168 4
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-154 genes (present in the 3 experiments)
-
-\subsubsection{figure}
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{area1dginn}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-\hlstd{area2hawk}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-\hlstd{area3coop}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-
-
-\hlstd{n12}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-
-\hlstd{n23}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-
-\hlstd{n13}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-
-
-\hlstd{n123}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-
-\hlkwd{draw.triple.venn}\hlstd{(area1dginn, area2hawk, area3coop,}
-\hlstd{n12, n23, n13, n123,}
-\hlkwc{category}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN-Young-bats"}\hlstd{,} \hlstr{"Hawkins-bats"}\hlstd{,} \hlstr{"Cooper-bats"}\hlstd{))}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/vennbats-1}
-\begin{kframe}\begin{verbatim}
-## (polygon[GRID.polygon.852], polygon[GRID.polygon.853], polygon[GRID.polygon.854], polygon[GRID.polygon.855], polygon[GRID.polygon.856], polygon[GRID.polygon.857], text[GRID.text.858], text[GRID.text.859], text[GRID.text.860], text[GRID.text.861], text[GRID.text.862], text[GRID.text.863], text[GRID.text.864], text[GRID.text.865], text[GRID.text.866], text[GRID.text.867])
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-\subsection{Mondrian}
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{library}\hlstd{(Mondrian)}
-
-\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
-\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
-\hlstd{monddata}\hlopt{$}\hlstd{bats_hawkins}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
-\hlstd{monddata}\hlopt{$}\hlstd{bats_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
-
-\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{])}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/mondrianbats-1}
-
-\end{knitrout}
-
-\section{To do}
-
-Comparaison G4 pas G4
-
-\end{document}
-