add new tab alldginn

covid_comp_script0_table.Rnw

@@ -128,10 +128,33 @@ names(dginnT)<-c("File", "Name", "Gene.name", "GeneSize",
   "dginn-primate_codemlM7M8.PSS")
 @
 
+<<eval=FALSE>>=
+table(dginnT$`dginn-primate_BUSTED`)
+table(dginnT$`dginn-primate_codemlM1M2`)
+table(dginnT$`dginn-primate_codemlM7M8`)
+table(dginnT$`dginn-primate_BppM1M2`)
+table(dginnT$`dginn-primate_BppM7M8`)
+
+table(dginnT$`dginn-primate_BUSTED`=="na",dginnT$`dginn-primate_codemlM1M2`=="na", dginnT$`dginn-primate_codemlM7M8`=="na", 
+      dginnT$`dginn-primate_BppM1M2`=="na", dginnT$`dginn-primate_BppM7M8`=="na" )
+
+@
+
+
+
 \subsection{Join Table and DGINN table}
 
 <<>>=
 tab<-merge(tab,dginnT, by="Gene.name", all.x=T)
+
+table(tab$`dginn-primate_BUSTED`)
+table(tab$`dginn-primate_codemlM1M2`)
+table(tab$`dginn-primate_codemlM7M8`)
+table(tab$`dginn-primate_BppM1M2`)
+table(tab$`dginn-primate_BppM7M8`)
+table(tab$`dginn-primate_BUSTED`=="na" | tab$`dginn-primate_codemlM1M2`=="na" | tab$`dginn-primate_codemlM7M8`=="na" | 
+      tab$`dginn-primate_BppM1M2`=="na"| tab$`dginn-primate_BppM7M8`=="na" )
+
 @
 
 \subsection{Add DGINN results on bat dataset}
@@ -153,7 +176,6 @@ dginnbatsnew2<-read.delim(paste0(workdir,
 	    fill=T, h=T)
 
 # colomne choice, BUSTED and Bppml form first file, codeml from the other one
-
 dginnbatsnew<-dginnbatsnew1
 dginnbatsnew$omegaM0codeml<-dginnbatsnew2$omegaM0codeml
 
@@ -245,5 +267,219 @@ tab<-merge(tab,dginnbats, by="cooper.batsGene", all.x=T)
 write.table(tab, "covid_comp_complete.txt", row.names=FALSE, quote=FALSE, sep="\t")
 @
 
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+\section{Second Table}
+
+Table containing the DGINN results for both Primates and bats. Conserve all genes.
+
+\subsection{Primates}
+
+<<>>=
+dginnT<-read.delim(paste0(workdir,
+      "data/DGINN_202005281649summary_cleaned.csv"), 
+      fill=T, h=T, sep=",")
+
+dim(dginnT)
+names(dginnT)
+
+# Rename the columns to include primate
+names(dginnT)<-c("File", "Name", "Gene.name", "GeneSize", 
+  "dginn-primate_NbSpecies", "dginn-primate_omegaM0Bpp",
+  "dginn-primate_omegaM0codeml", "dginn-primate_BUSTED", 
+  "dginn-primate_BUSTED.p.value", "dginn-primate_MEME.NbSites", 
+  "dginn-primate_MEME.PSS", "dginn-primate_BppM1M2",           
+  "dginn-primate_BppM1M2.p.value", "dginn-primate_BppM1M2.NbSites",   
+  "dginn-primate_BppM1M2.PSS", "dginn-primate_BppM7M8",            
+  "dginn-primate_BppM7M8.p.value", "dginn-primate_BppM7M8.NbSites",   
+  "dginn-primate_BppM7M8.PSS",  "dginn-primate_codemlM1M2",         
+  "dginn-primate_codemlM1M2.p.value", "dginn-primate_codemlM1M2.NbSites", 
+  "dginn-primate_codemlM1M2.PSS",     "dginn-primate_codemlM7M8",        
+  "dginn-primate_codemlM7M8.p.value", "dginn-primate_codemlM7M8.NbSites", 
+  "dginn-primate_codemlM7M8.PSS")
+@
+
+\subsection{Bats}
+
+<<>>=
+# original table
+dginnbats<-read.delim(paste0(workdir,
+      "data/DGINN_202005281339summary_cleaned-LE201108.txt"),         
+		  fill=T, h=T)
+
+# rerun on corrected alignment
+dginnbatsnew<-read.delim(paste0(workdir,
+      "data/DGINN_202011262248_hyphybpp-202012192053_codeml-summary.txt"),
+	    fill=T, h=T)
+
+@
+<<>>=
+# Add both columns 
+dginnbatsnew$Lucie.s.comments<-""
+dginnbatsnew$Action.taken<-""
+
+# Homogenize column names
+dginnbats$BUSTED_p.value<-dginnbats$BUSTED.p.value
+dginnbats$MEME_NbSites<-dginnbats$MEME.NbSites
+dginnbats$MEME_PSS<-dginnbats$MEME.PSS   
+
+dginnbats$BppM1M2_p.value<-dginnbats$BppM1M2.p.value
+dginnbats$BppM1M2_NbSites<-dginnbats$BppM1M2.NbSites
+dginnbats$BppM1M2_PSS<-dginnbats$BppM1M2.PSS
+
+dginnbats$BppM7M8_p.value<-dginnbats$BppM7M8.p.value
+dginnbats$BppM7M8_NbSites<-dginnbats$BppM7M8.NbSites
+dginnbats$BppM7M8_PSS<-dginnbats$BppM7M8.PSS
+
+dginnbats$codemlM1M2_p.value<-dginnbats$codemlM1M2.p.value
+dginnbats$codemlM1M2_NbSites<-dginnbats$codemlM1M2.NbSites
+dginnbats$codemlM1M2_PSS<-dginnbats$codemlM1M2.PSS
+
+dginnbats$codemlM7M8_p.value<-dginnbats$codemlM7M8.p.value
+dginnbats$codemlM7M8_NbSites<-dginnbats$codemlM7M8.NbSites
+dginnbats$codemlM7M8_PSS<-dginnbats$codemlM7M8.PSS
+@
+
+<<>>=
+# Order columns in the same order in both tables
+dginnbats<-dginnbats[,names(dginnbatsnew)]
+
+names(dginnbatsnew) %in% names(dginnbats)
+names(dginnbats)==names(dginnbatsnew)
+
+# Put RIPK aside
+ripk1<-dginnbatsnew[dginnbatsnew$Gene=="RIPK1",1:27]
+
+# Add it to primate table
+names(ripk1)<-names(dginnT)
+
+ripk1$`dginn-primate_omegaM0Bpp`<-as.factor(ripk1$`dginn-primate_omegaM0Bpp`)
+ripk1$`dginn-primate_BUSTED.p.value`<-as.factor(ripk1$`dginn-primate_BUSTED.p.value`)
+ripk1$`dginn-primate_BppM1M2.p.value`<-as.factor(ripk1$`dginn-primate_BppM1M2.p.value`)
+ripk1$`dginn-primate_BppM7M8.p.value`<-as.factor(ripk1$`dginn-primate_BppM7M8.p.value`)
+
+dginnT<-rbind(dginnT, ripk1)
+
+## Remove it Ripk1 from bats
+dginnbatsnew<-dginnbatsnew[dginnbatsnew$Gene!="RIPK1",]
+
+
+## suppress redundant lines
+dginnbats<-dginnbats[(dginnbats$Gene %in% dginnbatsnew$Gene)==FALSE,]
+names(dginnbatsnew)<-names(dginnbats)
+
+## replace by new data
+dginnbatsnew$omegaM0Bpp<-as.factor(dginnbatsnew$omegaM0Bpp)
+dginnbatsnew$BppM1M2_p.value<-as.factor(dginnbatsnew$BppM1M2_p.value)
+dginnbatsnew$BppM7M8_p.value<-as.factor(dginnbatsnew$BppM7M8_p.value)
+
+dginnbats<-rbind(dginnbats, dginnbatsnew)
+
+names(dginnbats)<-c("bats_File", "bats_Name", "Gene.name", paste0("bats_", 
+    names(dginnbats)[-(1:3)]))
+names(dginnbats)
+
+@
+
+\subsection{Merged table}
+<<setup, include=FALSE, cache=FALSE, tidy=TRUE>>=
+options(tidy=TRUE, width=70)
+@
+<<>>=
+#tidy.opts = list(width.cutoff = 60)
+dim(dginnT)
+dginnT$Gene.name
+dim(dginnbats)
+dginnbats$Gene.name
+@
+
+Manual corrections:
+
+TMPRSS2 in bats
+<<>>=
+dginnbats[dginnbats$Gene.name=="TMPRSS2",]
+# keeping the uncut one
+# renaming the other one TMPRSS2_cut
+dginnbats[dginnbats$bats_File=="TMPRSS2_bat_select_cut_mafft_prank","Gene.name"]<-"TMPRSS2_cut"
+@
+
+RIPK1: ANcestral version kept, suppress it "RIPK1\_sequences\_filtered\_longestORFs\_mafft\_mincov\_prank"
+<<>>=
+dginnT<-dginnT[dginnT$File!="RIPK1_sequences_filtered_longestORFs_mafft_mincov_prank",]
+@
+
+REEP6 eA et B
+<<>>=
+dginnbats$Gene.name<-as.character(dginnbats$Gene.name)
+dginnbats[dginnbats$bats_File=="REEP6_sequences_filtered_longestORFs_D210gp1_prank", "Gene.name"]<-"REEP6_old"
+dginnbats[dginnbats$bats_File=="REEP6_LA_bat_select_mafft_prank", "Gene.name"]<-"REEP6"
+dginnbats[dginnbats$bats_File=="REEP6_LB_bat_select_mafft_prank", "Gene.name"]<-"REEP6_like"
+@
+
+GNG5
+<<>>=
+dginnT$Gene.name<-as.character(dginnT$Gene.name)
+dginnT[dginnT$File=="GNG5_sequences_filtered_longestORFs_D189gp2_prank", "Gene.name"]<-"GNG5_like"
+@
+
+
+<<>>=
+dim(dginnbats)
+dim(dginnT)
+
+# genes in common
+dginnT$Gene.name[dginnT$Gene.name %in% dginnbats$Gene.name]
+length(dginnT$Gene.name[dginnT$Gene.name %in% dginnbats$Gene.name])
+
+# genes only in primates
+dginnT$Gene.name[(dginnT$Gene.name %in% dginnbats$Gene.name)==FALSE]
+length(dginnT$Gene.name[(dginnT$Gene.name %in% dginnbats$Gene.name)==FALSE])
+
+# genes only in bats
+dginnbats$Gene.name[(dginnbats$Gene.name %in% dginnT$Gene.name)==FALSE]
+length(dginnbats$Gene.name[(dginnbats$Gene.name %in% dginnT$Gene.name)==FALSE])
+
+@
+
+<<>>=
+tab<-merge(dginnT, dginnbats, by="Gene.name", all.x=T, all.y=T)
+dim(tab)
+
+write.table(tab, "covid_comp_alldginn.txt", sep="\t")
+@
+
+
 \end{document}