add column in alldginn

covid_comp_script0_table.tex

@@ -1066,9 +1066,11 @@ TMPRSS2 in bats
 \begin{alltt}
 \hlcom{# keeping the uncut one}
 \hlcom{# renaming the other one TMPRSS2_cut}
-\hlstd{dginnbats[dginnbats}\hlopt{$}\hlstd{bats.File}\hlopt{==}\hlstr{"TMPRSS2_bat_select_cut_mafft_prank"}\hlstd{,}\hlstr{"Gene.name"}\hlstd{]}\hlkwb{<-}\hlstr{"TMPRSS2_cut"}
+\hlstd{dginnbats[dginnbats}\hlopt{$}\hlstd{bats_File}\hlopt{==}\hlstr{"TMPRSS2_bat_select_cut_mafft_prank"}\hlstd{,}\hlstr{"Gene.name"}\hlstd{]}\hlkwb{<-}\hlstr{"TMPRSS2_cut"}
 \end{alltt}
-\end{kframe}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning in `[<-.factor`(`*tmp*`, iseq, value = "{}TMPRSS2\_cut"{}): invalid factor level, NA generated}}\end{kframe}
 \end{knitrout}
 
 RIPK1: ANcestral version kept, suppress it "RIPK1\_sequences\_filtered\_longestORFs\_mafft\_mincov\_prank"
@@ -1119,7 +1121,8 @@ GNG5
 \end{verbatim}
 \begin{alltt}
 \hlcom{# genes in common}
-\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name]}
+\hlstd{common}\hlkwb{<-}\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name]}
+\hlstd{common}
 \end{alltt}
 \begin{verbatim}
 ##   [1] "AAR2"      "AASS"      "AATF"      "ABCC1"     "ACAD9"    
@@ -1196,7 +1199,8 @@ GNG5
 \end{verbatim}
 \begin{alltt}
 \hlcom{# genes only in primates}
-\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[(dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\hlstd{onlyprimates}\hlkwb{<-}\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[(dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\hlstd{onlyprimates}
 \end{alltt}
 \begin{verbatim}
 ##  [1] "ADAM9[0-3120]"      "ADAM9[3119-3927]"   "ATP5MGL"           
@@ -1238,7 +1242,8 @@ GNG5
 \end{verbatim}
 \begin{alltt}
 \hlcom{# genes only in bats}
-\hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name[(dginnbats}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\hlstd{onlybats}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name[(dginnbats}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\hlstd{onlybats}
 \end{alltt}
 \begin{verbatim}
 ##  [1] "ADAM9[0-2769]"      "ADAM9[2768-3030]"   "ARL6IP6"           
@@ -1250,16 +1255,45 @@ 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"
+## [28] "REEP6_like"         "SELENOS"            NA
 \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] 29
+## [1] 30
 \end{verbatim}
 \end{kframe}
 \end{knitrout}
 
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(dginnT, dginnbats,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{,} \hlkwc{all.x}\hlstd{=T,} \hlkwc{all.y}\hlstd{=T)}
+\hlkwd{dim}\hlstd{(tab)}
+\end{alltt}
+\begin{verbatim}
+## [1] 442  55
+\end{verbatim}
+\begin{alltt}
+\hlcom{# add column "shared"/"only bats"/"only primates"}
+\hlstd{tab}\hlopt{$}\hlstd{status}\hlkwb{<-}\hlstr{""}
+\hlstd{tab}\hlopt{$}\hlstd{status[tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{common]}\hlkwb{<-}\hlstr{"shared"}
+\hlstd{tab}\hlopt{$}\hlstd{status[tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{onlyprimates]}\hlkwb{<-}\hlstr{"onlyprimates"}
+\hlstd{tab}\hlopt{$}\hlstd{status[tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{onlybats]}\hlkwb{<-}\hlstr{"onlybats"}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{status)}
+\end{alltt}
+\begin{verbatim}
+## 
+##     onlybats onlyprimates       shared 
+##           30           89          323
+\end{verbatim}
+\begin{alltt}
+\hlkwd{write.table}\hlstd{(tab,} \hlstr{"covid_comp_alldginn.txt"}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
 \end{document}