Commit 762975f5 authored by mcariou's avatar mcariou
Browse files

add selenos to tables

parent 224275b3
......@@ -364,7 +364,7 @@ But Genetic Innovation by splicing variants YES.
" "" "onlybats"
"350" "SCCPDH" "SCCPDH_sequences_filtered_longestORFs_mafft_mincov_prank" "SCCPDH_all" 717 23 "0.297146699972" "0.323" "Y" "0.0242" 4 "203, 437, 632, 635" "N" "0.16718066834449946" 0 "na" "N" "0.05798336825737528" 0 "na" "Y" "0.03951796106177764" 1 "590" "Y" "0.015732919159708345" 1 "590" "SCCPDH_sequences_filtered_longestORFs_mafft_prank" "SCCPDH" 654 12 "0.281129406592" "0.291" "N" 0.1315 11 "46, 70, 87, 228, 229, 231, 238, 327, 379, 594, 644" "N" "0.0747269312417341" 0 "na" "Y" "0.005045637026761042" 1 "367" "Y" "0.047028569511397056" 0 "" "Y" "0.0063709925831932045" 1 "367" "PS ok. Splice variants" "" "shared"
"351" "SDF2" "SDF2_sequences_filtered_longestORFs_mafft_mincov_prank" "SDF2_all" 364 23 "0.091229165614" "0.089" "N" "0.7862" 0 "na" "N" "0.9999997541511068" 0 "na" "N" "0.9999998942125841" 0 "na" "N" "1.0" 0 "na" "N" "0.9990004998331715" 0 "na" "SDF2_bat_select_mafft_prank" "SDF2" 246 12 "0.082797829312181" "0.080" "N" 0.2145 0 "na" "N" "0.999999439606811" 0 "na" "N" "0.999999993020992" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "" "" "shared"
"352" "SELENOS" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "SELENOS_bat_select_mafft_prank" "SELENOS" 218 8 "0.1693975661318" "0.172" "N" 0.8176 5 "71, 72, 85, 128, 173" "N" "0.999999579118228" 0 "na" "N" "0.389714156459387" 0 "na" "N" "0.9970044955034437" 0 "na" "N" "0.2133118712228997" 0 "na" "" "" "onlybats"
"352" "SELENOS" "SELENOS_sequences_filtered_longestORFs_mafft_mincov_prank" "SELENOS_all" 367 24 "0.207287174753623" "0.196" "Y" "0" 1 "90" "N" "0.999999228305" 0 "na" "N" "0.986116909613" 0 "na" "N" "1" 0 "na" "N" "0.692117181689" 0 "na" "SELENOS_bat_select_mafft_prank" "SELENOS" 218 8 "0.1693975661318" "0.172" "N" 0.8176 5 "71, 72, 85, 128, 173" "N" "0.999999579118228" 0 "na" "N" "0.389714156459387" 0 "na" "N" "0.9970044955034437" 0 "na" "N" "0.2133118712228997" 0 "na" "" "" "shared"
"353" "SELENOS[0-927]" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "SELENOS_sequences_filtered_longestORFs_mafft_prank_frag0to927" "SELENOS[0-927]" 309 11 "0.213235744659" "0.250" "Y" 0.0085 3 "126, 148, 154" "N" "0.3022734485269354" 0 "na" "N" "0.1168296305173564" 0 "na" "N" "1.0" 0 "na" "N" "0.24268280925769264" 0 "na" "Recomb triggered by aln with lots of indels" "" "onlybats"
"354" "SELENOS[926-1137]" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "SELENOS_sequences_filtered_longestORFs_mafft_prank_frag926to1137" "SELENOS[926-1137]" 70 11 "0.233147569842" "0.246" "N" 1 0 "na" "N" "0.9999999153342323" 0 "na" "N" "0.9999906640992244" 0 "na" "N" "0.9694755730759651" 0 "na" "N" "0.3348743138811512" 0 "na" "" "" "onlybats"
"355" "SEPSECS" "SEPSECS_sequences_filtered_longestORFs_mafft_mincov_prank" "SEPSECS_all" 1204 24 "0.200383584131" "0.191" "Y" "0.0012" 4 "411, 792, 871, 1131" "Y" "0.04699410636855563" 1 "871" "Y" "0.000675790377354786" 1 "871" "Y" "0.022573017543302893" 0 "" "Y" "0.002544044860029952" 1 "871" "SEPSECS_sequences_filtered_longestORFs_mafft_prank" "SEPSECS" 642 12 "0.207760285718" "0.221" "Y" 0.0113 0 "na" "N" "0.4067707665111908" 0 "na" "Y" "0.00326458340100601" 2 "577, 585" "N" "0.4269877306527835" 0 "na" "N" "0.0707218996108505" 0 "na" "" "" "shared"
......
......@@ -273,7 +273,7 @@ But Genetic Innovation by splicing variants YES.
"SCARB1" "SCARB1" "SCARB1" "nsp7" "SCARB1" "list26_COV_list4dataset2nonOrf" "scavenger receptor class B member 1" "CD36L1|CLA-1|CLA1|HDLQTL6|SR-BI|SRB1" "no" 25 1530 510 0.10383 0.62207 0.0784 0.7554 1 1 1 1 1 1 NA NA NA "" "" "" "" NA NA NA NA NA NA NA NA NA NA NA NA NA "" "SCARB1" "ENSG00000073060.15" "ENST00000545493.1" 14 146 100 0.221176368 0.1874 0.49354 0.49355 -910.195166 -910.195401 0.999765028 NA NA NA "" "SCARB1" 0.06378625 0.750735805 "" NA NA NA "" "" 1059 353 0.12908 0.34857 0.0509 0.3941 1 1 1 1 1 1 NA NA NA "" "SCARB1" "SCARB1_sequences_filtered_longestORFs_mafft_mincov_prank_part2_prank" "SCARB1_all_part2" 1623 24 "0.094947443872" "0.131" "Y" "0.0000" 11 "549, 607, 630, 703, 733, 911, 965, 993, 1432, 1531, 1622" "N" "0.9999999983037924" 0 "na" "N" "0.42297612986890076" 0 "na" "Y" "7.551887340080195e-27" 1 "1531" "na" "na" 0 "na" "SCARB1_sequences_filtered_longestORFs_mafft_prank" "SCARB1" 763 10 "0.218091439138" "0.155" "Y" 0 19 "5, 7, 132, 133, 137, 157, 176, 236, 277, 417, 476, 509, 592, 674, 688, 724, 740, 741, 763" "N" "0.9999998503026403" 0 "na" "N" "0.4515726499701246" 0 "na" "N" "1.0" 0 "na" "Y" "0.0002460440433622239" 1 "763" "PS. Splicing variants" "" "shared"
"SCCPDH" "SCCPDH" "SCCPDH" "nsp7" "SCCPDH" "list24_COV_list2nonOrf" "saccharopine dehydrogenase (putative)" "CGI-49|NET11" "no" 24 1290 430 0.26038 0.57846 0.1053 0.4043 1 1 1 1 1 1 NA NA NA "" "" "" "" NA NA NA NA NA NA NA NA NA NA NA NA NA "" "SCCPDH" "ENSG00000143653.9" "ENST00000366510.3" 15 430 97.6744186 0.196343201 0.1627 0.45905 0.45905 -2886.510879 -2886.510885 0.999994 NA NA NA "" "SCCPDH" 0.002019556 0.09129021 "" NA NA NA "" "" 999 333 0.29684 0.36519 0.074 0.2492 1 1 1 1 1 1 NA NA NA "" "SCCPDH" "SCCPDH_sequences_filtered_longestORFs_mafft_mincov_prank" "SCCPDH_all" 717 23 "0.297146699972" "0.323" "Y" "0.0242" 4 "203, 437, 632, 635" "N" "0.16718066834449946" 0 "na" "N" "0.05798336825737528" 0 "na" "Y" "0.03951796106177764" 1 "590" "Y" "0.015732919159708345" 1 "590" "SCCPDH_sequences_filtered_longestORFs_mafft_prank" "SCCPDH" 654 12 "0.281129406592" "0.291" "N" 0.1315 11 "46, 70, 87, 228, 229, 231, 238, 327, 379, 594, 644" "N" "0.0747269312417341" 0 "na" "Y" "0.005045637026761042" 1 "367" "Y" "0.047028569511397056" 0 "" "Y" "0.0063709925831932045" 1 "367" "PS ok. Splice variants" "" "shared"
"SDF2" "SDF2" "SDF2" "orf8" "SDF2" "list25_COV_list3dataset2orf" "stromal cell derived factor 2" "-" "no" 23 636 212 0.13507 0.3131 0.0364 0.2694 1 1 1 1 1 1 NA NA NA "" "SDF2" "ENSMLUG00000012419.2" "ENSMLUT00000012419.2" 15 212 98.58490566 0.06852197 0.335 0.90704 0.90706 -1790.437725 -1790.438975 0.998750781 NA NA NA "" "SDF2" "ENSG00000132581.9" "ENST00000591903.1" 19 105 88.57142857 0.073449063 4.3067 9.69242 9.69891 -726.542628 -726.543552 0.999076427 NA NA NA "" "SDF2" 0.997743245 1 "" NA NA NA "" "" 522 174 0.10167 0.24504 0.0225 0.2215 1 1 0.96895 1 1 1 NA NA NA "" "SDF2" "SDF2_sequences_filtered_longestORFs_mafft_mincov_prank" "SDF2_all" 364 23 "0.091229165614" "0.089" "N" "0.7862" 0 "na" "N" "0.9999997541511068" 0 "na" "N" "0.9999998942125841" 0 "na" "N" "1.0" 0 "na" "N" "0.9990004998331715" 0 "na" "SDF2_bat_select_mafft_prank" "SDF2" 246 12 "0.082797829312181" "0.080" "N" 0.2145 0 "na" "N" "0.999999439606811" 0 "na" "N" "0.999999993020992" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "" "" "shared"
"SELENOS" "SELENOS" "VIMP" "nsp7" "VIMP" "list26_COV_list4dataset2nonOrf" "selenoprotein S protein-coding" "AD-015|ADO15|SBBI8|SELS|SEPS1|VIMP" "no" 24 567 189 0.21832 0.68129 0.1108 0.5076 0.93424 1 0.91359 1 0.99621 1 NA NA NA "" "" "" "" NA NA NA NA NA NA NA NA NA NA NA NA NA "" "SELENOS" "ENSG00000131871.14" "ENST00000528346.1" 9 218 83.02752294 0.295972578 0.1231 0.34109 0.34109 -1105.646929 -1105.646929 1 NA NA NA "" "" NA NA "" NA NA NA "" "" 408 136 0.1532 0.50802 0.0684 0.4462 0.65661 1 0.78342 1 0.90578 1 NA NA NA "" "SELENOS" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "SELENOS_bat_select_mafft_prank" "SELENOS" 218 8 "0.1693975661318" "0.172" "N" 0.8176 5 "71, 72, 85, 128, 173" "N" "0.999999579118228" 0 "na" "N" "0.389714156459387" 0 "na" "N" "0.9970044955034437" 0 "na" "N" "0.2133118712228997" 0 "na" "" "" "onlybats"
"SELENOS" "SELENOS" "VIMP" "nsp7" "VIMP" "list26_COV_list4dataset2nonOrf" "selenoprotein S protein-coding" "AD-015|ADO15|SBBI8|SELS|SEPS1|VIMP" "no" 24 567 189 0.21832 0.68129 0.1108 0.5076 0.93424 1 0.91359 1 0.99621 1 NA NA NA "" "" "" "" NA NA NA NA NA NA NA NA NA NA NA NA NA "" "SELENOS" "ENSG00000131871.14" "ENST00000528346.1" 9 218 83.02752294 0.295972578 0.1231 0.34109 0.34109 -1105.646929 -1105.646929 1 NA NA NA "" "" NA NA "" NA NA NA "" "" 408 136 0.1532 0.50802 0.0684 0.4462 0.65661 1 0.78342 1 0.90578 1 NA NA NA "" "SELENOS" "SELENOS_sequences_filtered_longestORFs_mafft_mincov_prank" "SELENOS_all" 367 24 "0.207287174753623" "0.196" "Y" "0" 1 "90" "N" "0.999999228305" 0 "na" "N" "0.986116909613" 0 "na" "N" "1" 0 "na" "N" "0.692117181689" 0 "na" "SELENOS_bat_select_mafft_prank" "SELENOS" 218 8 "0.1693975661318" "0.172" "N" 0.8176 5 "71, 72, 85, 128, 173" "N" "0.999999579118228" 0 "na" "N" "0.389714156459387" 0 "na" "N" "0.9970044955034437" 0 "na" "N" "0.2133118712228997" 0 "na" "" "" "shared"
"SEPSECS" "SEPSECS" "SEPSECS" "nsp8" "SEPSECS" "list24_COV_list2nonOrf" "Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase" "LP|PCH2D|SLA|SLA/LP" "yes" 24 1506 502 0.23138 0.39192 0.0699 0.3022 0.00014539 0.0027987575 0.00073465 0.0104755648148148 0.00073013 0.0140550025 5.009 3.57509 6 "246_D_0.971,375_M_1.000,383_H_0.956,385_D_0.950,386_E_0.925,456_K_0.990" "SEPSECS" "ENSMLUG00000005883.2" "ENSMLUT00000005885.2" 11 505 92.07920792 0.157833305 0.327 0.84904 0.84915 -3816.572052 -3816.423878 0.862281065 NA NA NA "" "" "" "" NA NA NA NA NA NA NA NA NA NA NA NA NA "" "" NA NA "" NA NA NA "" "" 1296 432 0.24565 0.28571 0.0539 0.2196 8.3292e-06 0.000458106 4.8623e-05 0.002339981875 4.9379e-05 0.002715845 1.667 8.61509 5 "325_M_1.000,333_H_0.980,345_A_0.902,394_K_0.996,428_Y_0.910" "SEPSECS" "SEPSECS_sequences_filtered_longestORFs_mafft_mincov_prank" "SEPSECS_all" 1204 24 "0.200383584131" "0.191" "Y" "0.0012" 4 "411, 792, 871, 1131" "Y" "0.04699410636855563" 1 "871" "Y" "0.000675790377354786" 1 "871" "Y" "0.022573017543302893" 0 "" "Y" "0.002544044860029952" 1 "871" "SEPSECS_sequences_filtered_longestORFs_mafft_prank" "SEPSECS" 642 12 "0.207760285718" "0.221" "Y" 0.0113 0 "na" "N" "0.4067707665111908" 0 "na" "Y" "0.00326458340100601" 2 "577, 585" "N" "0.4269877306527835" 0 "na" "N" "0.0707218996108505" 0 "na" "" "" "shared"
"SIGMAR1" "SIGMAR1" "SIGMAR1" "nsp6" "SIGMAR1" "list26_COV_list4dataset2nonOrf" "sigma non-opioid intracellular receptor 1" "ALS16|DSMA2|OPRS1|SIG-1R|SR-BP|SR-BP1|SRBP|hSigmaR1|sigma1R" "no" 24 672 224 0.05548 0.42023 0.0297 0.5354 0.38838 0.874422807017544 0.596 1 0.67815 1 NA NA NA "" "SIGMAR1" "ENSMLUG00000003061.1" "ENSMLUT00000003059.1" 9 224 98.66071429 0.085786955 0.2738 0.68602 0.68531 -1513.500222 -1513.071044 0.651044033 NA NA NA "" "SIGMAR1" "ENSG00000147955.16" "ENST00000477726.1" 16 193 87.56476684 0.045269245 0.2398 0.42429 0.42002 -1002.547639 -1002.375629 0.841970753 NA NA NA "" "" NA NA "" NA NA NA "" "" 429 143 0.0585 0.29391 0.0203 0.3471 1 1 1 1 1 1 NA NA NA "" "SIGMAR1" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "SIGMAR1_sequences_filtered_longestORFs_mafft_prank" "SIGMAR1" 463 11 "0.063555782622" "0.062" "N" 1 0 "na" "N" "0.9999998523637823" 0 "na" "Y" "0.03935837746698778" 3 "28, 43, 296" "N" "1.0" 0 "na" "N" "0.3163202908753499" 0 "na" "" "" "onlybats"
"SIL1" "SIL1" "SIL1" "orf8" "SIL1" "list23_COV_list1orf" "SIL1 nucleotide exchange factor" "BAP|MSS|ULG5" "no" 24 1386 462 0.15942 0.59934 0.0829 0.52 0.12745 0.434232300884956 1 1 1 1 NA NA NA "" "SIL1" "ENSMLUG00000005198.2" "ENSMLUT00000005199.2" 11 385 98.44155844 0.116118369 0.3877 1.00231 1.00231 -3151.512186 -3151.512306 0.999880007 NA NA NA "" "SIL1" "ENSG00000120725.12" "ENST00000505353.1" 19 94 90.42553191 0.221006576 0.2776 0.74645 0.74672 -692.585908 -692.585983 0.999925003 NA NA NA "" "" NA NA "" NA NA NA "" "" 1059 353 0.20076 0.29004 0.047 0.2343 1 1 1 1 0.57402 1 NA NA NA "" "SIL1" "SIL1_sequences_filtered_longestORFs_mafft_mincov_prank" "SIL1_all" 586 24 "0.187714729747" "0.164" "N" "0.5261" 5 "98, 119, 143, 208, 560" "N" "0.9999991549406264" 0 "na" "N" "0.2610615228717177" 0 "na" "N" "1.0" 0 "na" "N" "0.5210027286033118" 0 "na" "SIL1_sequences_filtered_longestORFs_mafft_prank" "SIL1" 670 12 "0.168133221490" "0.160" "Y" 0 5 "212, 241, 273, 568, 647" "N" "0.8329986992390037" 0 "na" "N" "0.10828949711717219" 0 "na" "N" "0.3426656803484229" 0 "na" "N" "0.05535435177850455" 0 "na" "" "" "shared"
......
......@@ -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}
<<>>=
......
......@@ -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{)}
......
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