covid_comp_script0_table.Rnw

@@ -56,6 +56,43 @@ names(dginnT)<-c("File", "Name", "Gene.name", "GeneSize",
   "dginn-primate_codemlM7M8.PSS")
 @
 
+Add SELENOS
+
+<<selenos>>=
+selenos<-read.delim(paste0(workdir,
+      "data/resSELENOS.tab"))
+
+# liste of colonne
+
+colonnes<-c("File", "Name", "Gene", "GeneSize",
+  "NbSpecies", "omegaM0Bpp", "omegaM0codeml", "BUSTED",
+  "BUSTED_p.value",  "MEME_NbSites", "MEME_PSS", "BppM1M2",
+  "BppM1M2_p.value", "BppM1M2_NbSites", "BppM1M2_PSS", "BppM7M8", 
+  "BppM7M8_p.value", "BppM7M8_NbSites", "BppM7M8_PSS","codemlM1M2",
+  "codemlM1M2_p.value", "codemlM1M2_NbSites",  "codemlM1M2_PSS", "codemlM7M8",   
+  "codemlM7M8_p.value", "codemlM7M8_NbSites", "codemlM7M8_PSS")         
+
+selenos<-selenos[,colonnes]
+
+
+
+@
+
+<<>>=
+names(selenos)<-names(dginnT)
+selenos[,6]<-as.factor(selenos[,6])
+selenos[,9]<-as.factor(selenos[,9])
+selenos[,11]<-as.factor(selenos[,11])
+
+selenos[,13]<-as.factor(selenos[,13])
+selenos[,17]<-as.factor(selenos[,17])
+selenos[,21]<-as.factor(selenos[,21])
+selenos[,25]<-as.factor(selenos[,25])
+
+## convertir les pvalues
+dginnT<-rbind(dginnT, selenos)
+@
+    
 \subsection{Bats}
 
 <<>>=

covid_comp_script0_table.tex

@@ -115,6 +115,48 @@ Table containing the DGINN results for both Primates and bats. Conserve all gene
 \end{kframe}
 \end{knitrout}
 
+Add SELENOS
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{selenos}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+      \hlstr{"data/resSELENOS.tab"}\hlstd{))}
+
+\hlcom{# liste of colonne}
+
+\hlstd{colonnes}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"Name"}\hlstd{,} \hlstr{"Gene"}\hlstd{,} \hlstr{"GeneSize"}\hlstd{,}
+  \hlstr{"NbSpecies"}\hlstd{,} \hlstr{"omegaM0Bpp"}\hlstd{,} \hlstr{"omegaM0codeml"}\hlstd{,} \hlstr{"BUSTED"}\hlstd{,}
+  \hlstr{"BUSTED_p.value"}\hlstd{,}  \hlstr{"MEME_NbSites"}\hlstd{,} \hlstr{"MEME_PSS"}\hlstd{,} \hlstr{"BppM1M2"}\hlstd{,}
+  \hlstr{"BppM1M2_p.value"}\hlstd{,} \hlstr{"BppM1M2_NbSites"}\hlstd{,} \hlstr{"BppM1M2_PSS"}\hlstd{,} \hlstr{"BppM7M8"}\hlstd{,}
+  \hlstr{"BppM7M8_p.value"}\hlstd{,} \hlstr{"BppM7M8_NbSites"}\hlstd{,} \hlstr{"BppM7M8_PSS"}\hlstd{,}\hlstr{"codemlM1M2"}\hlstd{,}
+  \hlstr{"codemlM1M2_p.value"}\hlstd{,} \hlstr{"codemlM1M2_NbSites"}\hlstd{,}  \hlstr{"codemlM1M2_PSS"}\hlstd{,} \hlstr{"codemlM7M8"}\hlstd{,}
+  \hlstr{"codemlM7M8_p.value"}\hlstd{,} \hlstr{"codemlM7M8_NbSites"}\hlstd{,} \hlstr{"codemlM7M8_PSS"}\hlstd{)}
+
+\hlstd{selenos}\hlkwb{<-}\hlstd{selenos[,colonnes]}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{names}\hlstd{(selenos)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnT)}
+\hlstd{selenos[,}\hlnum{6}\hlstd{]}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(selenos[,}\hlnum{6}\hlstd{])}
+\hlstd{selenos[,}\hlnum{9}\hlstd{]}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(selenos[,}\hlnum{9}\hlstd{])}
+\hlstd{selenos[,}\hlnum{11}\hlstd{]}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(selenos[,}\hlnum{11}\hlstd{])}
+
+\hlstd{selenos[,}\hlnum{13}\hlstd{]}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(selenos[,}\hlnum{13}\hlstd{])}
+\hlstd{selenos[,}\hlnum{17}\hlstd{]}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(selenos[,}\hlnum{17}\hlstd{])}
+\hlstd{selenos[,}\hlnum{21}\hlstd{]}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(selenos[,}\hlnum{21}\hlstd{])}
+\hlstd{selenos[,}\hlnum{25}\hlstd{]}\hlkwb{<-}\hlkwd{as.factor}\hlstd{(selenos[,}\hlnum{25}\hlstd{])}
+
+\hlcom{## convertir les pvalues}
+\hlstd{dginnT}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnT, selenos)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+    
 \subsection{Bats}
 
 \begin{knitrout}
@@ -172,16 +214,14 @@ Table containing the DGINN results for both Primates and bats. Conserve all gene
 \hlkwd{names}\hlstd{(dginnbatsnew)} \hlopt{%in%} \hlkwd{names}\hlstd{(dginnbats)}
 \end{alltt}
 \begin{verbatim}
-##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
-## [14] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 ## [27] TRUE TRUE TRUE
 \end{verbatim}
 \begin{alltt}
 \hlkwd{names}\hlstd{(dginnbats)}\hlopt{==}\hlkwd{names}\hlstd{(dginnbatsnew)}
 \end{alltt}
 \begin{verbatim}
-##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
-## [14] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 ## [27] TRUE TRUE TRUE
 \end{verbatim}
 \begin{alltt}
@@ -218,21 +258,12 @@ Table containing the DGINN results for both Primates and bats. Conserve all gene
 \hlkwd{names}\hlstd{(dginnbats)}
 \end{alltt}
 \begin{verbatim}
-##  [1] "bats_File"               "bats_Name"              
-##  [3] "Gene.name"               "bats_GeneSize"          
-##  [5] "bats_NbSpecies"          "bats_omegaM0Bpp"        
-##  [7] "bats_omegaM0codeml"      "bats_BUSTED"            
-##  [9] "bats_BUSTED_p.value"     "bats_MEME_NbSites"      
-## [11] "bats_MEME_PSS"           "bats_BppM1M2"           
-## [13] "bats_BppM1M2_p.value"    "bats_BppM1M2_NbSites"   
-## [15] "bats_BppM1M2_PSS"        "bats_BppM7M8"           
-## [17] "bats_BppM7M8_p.value"    "bats_BppM7M8_NbSites"   
-## [19] "bats_BppM7M8_PSS"        "bats_codemlM1M2"        
-## [21] "bats_codemlM1M2_p.value" "bats_codemlM1M2_NbSites"
-## [23] "bats_codemlM1M2_PSS"     "bats_codemlM7M8"        
-## [25] "bats_codemlM7M8_p.value" "bats_codemlM7M8_NbSites"
-## [27] "bats_codemlM7M8_PSS"     "bats_Lucie.s.comments"  
-## [29] "bats_Action.taken"
+##  [1] "bats_File"               "bats_Name"               "Gene.name"               "bats_GeneSize"           "bats_NbSpecies"         
+##  [6] "bats_omegaM0Bpp"         "bats_omegaM0codeml"      "bats_BUSTED"             "bats_BUSTED_p.value"     "bats_MEME_NbSites"      
+## [11] "bats_MEME_PSS"           "bats_BppM1M2"            "bats_BppM1M2_p.value"    "bats_BppM1M2_NbSites"    "bats_BppM1M2_PSS"       
+## [16] "bats_BppM7M8"            "bats_BppM7M8_p.value"    "bats_BppM7M8_NbSites"    "bats_BppM7M8_PSS"        "bats_codemlM1M2"        
+## [21] "bats_codemlM1M2_p.value" "bats_codemlM1M2_NbSites" "bats_codemlM1M2_PSS"     "bats_codemlM7M8"         "bats_codemlM7M8_p.value"
+## [26] "bats_codemlM7M8_NbSites" "bats_codemlM7M8_PSS"     "bats_Lucie.s.comments"   "bats_Action.taken"
 \end{verbatim}
 \end{kframe}
 \end{knitrout}
@@ -246,7 +277,7 @@ Table containing the DGINN results for both Primates and bats. Conserve all gene
 \hlkwd{dim}\hlstd{(dginnT)}
 \end{alltt}
 \begin{verbatim}
-## [1] 413  27
+## [1] 414  27
 \end{verbatim}
 \begin{alltt}
 \hlcom{#dginnT$Gene.name}
@@ -360,7 +391,7 @@ GNG5
 \hlkwd{dim}\hlstd{(dginnT)}
 \end{alltt}
 \begin{verbatim}
-## [1] 412  27
+## [1] 413  27
 \end{verbatim}
 \begin{alltt}
 \hlcom{# genes in common}
@@ -432,13 +463,13 @@ GNG5
 ## [306] "UBAP2"     "UBAP2L"    "UBXN8"     "UGGT2"     "UPF1"     
 ## [311] "USP54"     "VPS11"     "VPS39"     "WASHC4"    "WFS1"     
 ## [316] "YIF1A"     "ZC3H18"    "ZC3H7A"    "ZDHHC5"    "ZNF318"   
-## [321] "ZNF503"    "ZYG11B"    "RIPK1"
+## [321] "ZNF503"    "ZYG11B"    "SELENOS"   "RIPK1"
 \end{verbatim}
 \begin{alltt}
 \hlkwd{length}\hlstd{(dginnT}\hlopt{$}\hlstd{Gene.name[dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name])}
 \end{alltt}
 \begin{verbatim}
-## [1] 323
+## [1] 324
 \end{verbatim}
 \begin{alltt}
 \hlcom{# genes only in primates}
@@ -498,13 +529,13 @@ GNG5
 ## [19] "SIGMAR1"            "SLC44A2[0-2820]"    "SLC44A2[2819-3792]"
 ## [22] "TLE5"               "USP13"              "ZC3H18[0-1101]"    
 ## [25] "ZC3H18[1100-3678]"  "FGFR1OP"            "ELOB"              
-## [28] "REEP6_like"         "SELENOS"            "TMPRSS2_cut"
+## [28] "REEP6_like"         "TMPRSS2_cut"
 \end{verbatim}
 \begin{alltt}
 \hlkwd{length}\hlstd{(dginnbats}\hlopt{$}\hlstd{Gene.name[(dginnbats}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
 \end{alltt}
 \begin{verbatim}
-## [1] 30
+## [1] 29
 \end{verbatim}
 \end{kframe}
 \end{knitrout}
@@ -529,7 +560,7 @@ GNG5
 \begin{verbatim}
 ## 
 ##     onlybats onlyprimates       shared 
-##           30           89          323
+##           29           89          324
 \end{verbatim}
 \begin{alltt}
 \hlkwd{write.table}\hlstd{(tab,} \hlstr{"covid_comp_alldginn.txt"}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}