Commit 040507e4 authored by mcariou's avatar mcariou
Browse files

add column in alldginn

parent 60b706f7
This diff is collapsed.
......@@ -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}
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