Commit 696188c4 authored by mcariou's avatar mcariou
Browse files

correction compte de Y dans covid_comp_dataset.Rnw

parent 8cc0d97d
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......@@ -60,7 +60,7 @@ batstmp<-rowSums(cbind(tmp$bats_codemlM1M2=="Y", tmp$bats_codemlM7M8=="Y",
tmp$bats_BppM1M2=="Y", tmp$bats_BppM7M8=="Y", tmp$bats_BUSTED=="Y"))
primatetmp<-rowSums(cbind(tmp$"dginn.primate_codemlM1M2"=="Y",
tmp$"dginn.primat_codemlM7M8"=="Y", tmp$"dginn.primate_BppM1M2"=="Y",
tmp$"dginn.primate_codemlM7M8"=="Y", tmp$"dginn.primate_BppM1M2"=="Y",
tmp$"dginn.primate_BppM7M8"=="Y", tmp$"dginn.primate_BUSTED"=="Y"))
monddata$bats_dginn3<-ifelse(batstmp>=3, 1,0)
......
No preview for this file type
......@@ -126,7 +126,7 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlstd{tmp}\hlopt{$}\hlstd{bats_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{))}
\hlstd{primatetmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tmp}\hlopt{$}\hlstr{"dginn.primate_codemlM1M2"}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tmp}\hlopt{$}\hlstr{"dginn.primat_codemlM7M8"}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstr{"dginn.primate_BppM1M2"}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tmp}\hlopt{$}\hlstr{"dginn.primate_codemlM7M8"}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstr{"dginn.primate_BppM1M2"}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tmp}\hlopt{$}\hlstr{"dginn.primate_BppM7M8"}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstr{"dginn.primate_BUSTED"}\hlopt{==}\hlstr{"Y"}\hlstd{))}
\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn3}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(batstmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
......@@ -191,7 +191,9 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
## 78 GOLGA7 1 1 1 1
## 89 IDE 1 1 1 1
## 94 ITGB1 1 1 1 1
## 97 LMAN2 1 1 1 1
## 132 POLA1 1 1 1 1
## 164 SLC27A2 1 1 1 1
## 188 TOR1AIP1 1 1 1 1
## 201 VPS39 1 1 1 1
\end{verbatim}
......@@ -214,9 +216,10 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
## 78 GOLGA7 1 1 1 1
## 89 IDE 1 1 1 1
## 94 ITGB1 1 1 1 1
## 97 LMAN2 1 1 1 0
## 97 LMAN2 1 1 1 1
## 104 MOV10 1 1 0 0
## 132 POLA1 1 1 1 1
## 164 SLC27A2 1 1 1 0
## 164 SLC27A2 1 1 1 1
## 188 TOR1AIP1 1 1 1 1
## 201 VPS39 1 1 1 1
\end{verbatim}
......@@ -236,12 +239,28 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\begin{verbatim}
## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 20 CDK5RAP2 1 1 0 1
## 23 CEP135 0 1 0 1
## 26 CEP68 0 1 0 1
## 32 CLIP4 0 1 0 1
## 45 DPH5 0 1 0 1
## 50 EMC1 0 1 0 1
## 68 FYCO1 0 1 0 1
## 74 GIGYF2 0 1 0 1
## 75 GLA 0 1 0 1
## 83 HECTD1 0 1 0 1
## 95 LARP1 0 1 0 1
## 108 MYCBP2 0 1 0 1
## 111 NDUFB9 0 1 0 1
## 138 PRKAR2A 0 1 0 1
## 153 RIPK1 0 1 0 1
## 156 SAAL1 0 1 0 1
## 160 SEPSECS 0 1 0 1
## 162 SIRT5 0 1 0 1
## 163 SLC25A21 0 1 0 1
## 185 TMEM39B 0 1 0 1
## 191 TUBGCP2 0 1 0 1
## 194 UBAP2 0 1 0 1
## 197 UGGT2 0 1 0 1
## 204 ZNF318 0 1 0 1
\end{verbatim}
\end{kframe}
......@@ -256,30 +275,46 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\end{alltt}
\begin{verbatim}
## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 23 CEP135 0 1 0 0
## 23 CEP135 0 1 0 1
## 26 CEP68 0 1 0 1
## 32 CLIP4 0 1 0 0
## 32 CLIP4 0 1 0 1
## 33 CNTRL 0 1 0 0
## 45 DPH5 0 1 0 0
## 45 DPH5 0 1 0 1
## 50 EMC1 0 1 0 1
## 56 EXOSC2 0 1 0 0
## 68 FYCO1 0 1 0 1
## 74 GIGYF2 0 1 0 0
## 75 GLA 0 1 0 0
## 74 GIGYF2 0 1 0 1
## 75 GLA 0 1 0 1
## 79 GOLGB1 0 1 0 0
## 80 GORASP1 0 1 0 0
## 83 HECTD1 0 1 0 1
## 95 LARP1 0 1 0 0
## 95 LARP1 0 1 0 1
## 96 LARP7 0 1 0 0
## 100 MDN1 0 1 0 0
## 107 MRPS5 0 1 0 0
## 108 MYCBP2 0 1 0 1
## 111 NDUFB9 0 1 0 0
## 138 PRKAR2A 0 1 0 0
## 153 RIPK1 0 1 0 0
## 156 SAAL1 0 1 0 0
## 111 NDUFB9 0 1 0 1
## 115 NGLY1 0 1 0 0
## 118 NPC2 0 1 0 0
## 127 PITRM1 0 1 0 0
## 128 PLAT 0 1 0 0
## 134 POR 0 1 0 0
## 138 PRKAR2A 0 1 0 1
## 144 RAB14 0 1 0 0
## 145 RAB2A 0 1 0 0
## 153 RIPK1 0 1 0 1
## 156 SAAL1 0 1 0 1
## 160 SEPSECS 0 1 0 1
## 162 SIRT5 0 1 0 0
## 163 SLC25A21 0 1 0 0
## 185 TMEM39B 0 1 0 0
## 191 TUBGCP2 0 1 0 0
## 194 UBAP2 0 1 0 0
## 197 UGGT2 0 1 0 0
## 162 SIRT5 0 1 0 1
## 163 SLC25A21 0 1 0 1
## 172 STOM 0 1 0 0
## 181 TIMM8B 0 1 0 0
## 185 TMEM39B 0 1 0 1
## 189 TRIM59 0 1 0 0
## 190 TRMT1 0 1 0 0
## 191 TUBGCP2 0 1 0 1
## 194 UBAP2 0 1 0 1
## 197 UGGT2 0 1 0 1
## 199 USP54 0 1 0 0
## 204 ZNF318 0 1 0 1
\end{verbatim}
......@@ -302,8 +337,6 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
## 52 ERGIC1 1 0 1 0
## 91 IMPDH2 1 0 1 0
## 92 INHBE 1 0 1 0
## 97 LMAN2 1 1 1 0
## 164 SLC27A2 1 1 1 0
## 166 SLC44A2 1 0 1 0
## 177 TBK1 1 0 1 0
\end{verbatim}
......@@ -325,7 +358,6 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
## 82 GRPEL1 1 0 0 0
## 91 IMPDH2 1 0 1 0
## 92 INHBE 1 0 1 0
## 104 MOV10 1 0 0 0
## 120 NUP214 1 0 0 0
## 136 PRIM1 1 0 0 0
## 165 SLC30A9 1 0 0 0
......@@ -419,9 +451,9 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\end{alltt}
\begin{verbatim}
## [1] 0 1
## [1] 1 2
## [1] 2 0
## [1] 2 1
## [1] 3 1
\end{verbatim}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{1}\hlstd{]}
......@@ -433,8 +465,10 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{1.7}\hlstd{,} \hlstr{"p=1/n=1"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.6}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{18}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{2}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.8}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\end{alltt}
{\ttfamily\noindent\bfseries\color{errorcolor}{\#\# Error in seq.default(from = 0.1, to = 2, length.out = length(tmp) - 18): 'length.out' must be a non-negative number}}\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{0}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{2.2}\hlstd{,} \hlstr{"p=0/n=0"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{17}\hlstd{),}\hlopt{-}\hlnum{2.1}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{17}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
......@@ -443,11 +477,15 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{2} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{0}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{2.7}\hlstd{,} \hlstr{"p=0/n=2"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{18}\hlstd{),}\hlopt{-}\hlnum{2.6}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{18}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{2.8}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/tablo-1}
\begin{kframe}\begin{alltt}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{2.8}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\end{alltt}
{\ttfamily\noindent\bfseries\color{errorcolor}{\#\# Error in seq.default(from = 0.1, to = 1, length.out = length(tmp) - 18): 'length.out' must be a non-negative number}}\end{kframe}
\end{knitrout}
\end{document}
......
......@@ -185,14 +185,10 @@ I will merge the 2 tables.
\hlkwd{names}\hlstd{(dginnT)}
\end{alltt}
\begin{verbatim}
## [1] "File" "Name" "Gene"
## [4] "GeneSize" "NbSpecies" "omegaM0Bpp"
## [7] "omegaM0codeml" "BUSTED" "BUSTED.p.value"
## [10] "MEME.NbSites" "MEME.PSS" "BppM1M2"
## [13] "BppM1M2.p.value" "BppM1M2.NbSites" "BppM1M2.PSS"
## [16] "BppM7M8" "BppM7M8.p.value" "BppM7M8.NbSites"
## [19] "BppM7M8.PSS" "codemlM1M2" "codemlM1M2.p.value"
## [22] "codemlM1M2.NbSites" "codemlM1M2.PSS" "codemlM7M8"
## [1] "File" "Name" "Gene" "GeneSize" "NbSpecies" "omegaM0Bpp"
## [7] "omegaM0codeml" "BUSTED" "BUSTED.p.value" "MEME.NbSites" "MEME.PSS" "BppM1M2"
## [13] "BppM1M2.p.value" "BppM1M2.NbSites" "BppM1M2.PSS" "BppM7M8" "BppM7M8.p.value" "BppM7M8.NbSites"
## [19] "BppM7M8.PSS" "codemlM1M2" "codemlM1M2.p.value" "codemlM1M2.NbSites" "codemlM1M2.PSS" "codemlM7M8"
## [25] "codemlM7M8.p.value" "codemlM7M8.NbSites" "codemlM7M8.PSS"
\end{verbatim}
\begin{alltt}
......@@ -200,32 +196,24 @@ I will merge the 2 tables.
\hlstd{dginnT[(dginnT}\hlopt{$}\hlstd{Gene} \hlopt{%in%} \hlstd{tab}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlstd{F,}\hlstr{"Gene"}\hlstd{]}
\end{alltt}
\begin{verbatim}
## [1] ACE2 ADAM9[0-3120] ADAM9[3119-3927] ATP5MGL
## [5] C1H1ORF50 CEP135[0-3264] CEP135[3263-3678] CEP43
## [9] COQ8B COQ8A CSNK2A1 CSNK2B[0-609]
## [13] CSNK2B[608-2568] CYB5R1 DDX21[0-717] DDX21[716-2538]
## [17] DDX50 DNAJC15 DPH5[0-702] DPH5[701-1326]
## [21] DPY19L2 ELOC ERO1B EXOSC3[0-1446]
## [25] EXOSC3[1445-1980] FBN3 GNB4 GNB2
## [29] GNB3 GOLGA7[0-312] GOLGA7[311-549] GPX1[0-1218]
## [33] GPX1[1217-2946] HDAC1 HS6ST3 IMPDH1
## [37] ITGB1[0-2328] ITGB1[2327-2844] LMAN2L MRPS5[0-1569]
## [41] MRPS5[1568-3783] MARC2 MGRN1 NDFIP2[0-768]
## [45] NDFIP2[767-1314] NDUFAF2[0-258] NDUFAF2[257-744] NSD2
## [49] NUP58 NUP58[0-1824] NUP58[1823-2367] PABPC3
## [53] POTPABPC1 PABPC4L PABPC5 PCSK5
## [57] PRIM2[0-1071] PRIM2[1070-1902] PRKACB PRKACG
## [61] PTGES2[0-1587] PTGES2[1586-2202] RAB8B RAB13
## [65] RAB18[0-855] RAB18[854-1815] RAB2B RAB5A
## [69] RAB5B RAB15 RALB EZR
## [73] EZR[0-1458] EZR[1457-3771] MSN RETREG3
## [77] RHOB RHOC SLC44A2[0-2577] SLC44A2[2576-3657]
## [81] SPART SRP72[0-2604] SRP72[2603-3417] STOM[0-1047]
## [85] STOM[1046-1800] STOML3 TIMM29 TLE4
## [89] TLE2 TLE2[0-1302] TLE2[1301-3987] TMPRSS2
## [93] TOMM70 TOR1B WASHC4 WFS1[0-2346]
## [1] ACE2 ADAM9[0-3120] ADAM9[3119-3927] ATP5MGL C1H1ORF50 CEP135[0-3264]
## [7] CEP135[3263-3678] CEP43 COQ8B COQ8A CSNK2A1 CSNK2B[0-609]
## [13] CSNK2B[608-2568] CYB5R1 DDX21[0-717] DDX21[716-2538] DDX50 DNAJC15
## [19] DPH5[0-702] DPH5[701-1326] DPY19L2 ELOC ERO1B EXOSC3[0-1446]
## [25] EXOSC3[1445-1980] FBN3 GNB4 GNB2 GNB3 GOLGA7[0-312]
## [31] GOLGA7[311-549] GPX1[0-1218] GPX1[1217-2946] HDAC1 HS6ST3 IMPDH1
## [37] ITGB1[0-2328] ITGB1[2327-2844] LMAN2L MRPS5[0-1569] MRPS5[1568-3783] MARC2
## [43] MGRN1 NDFIP2[0-768] NDFIP2[767-1314] NDUFAF2[0-258] NDUFAF2[257-744] NSD2
## [49] NUP58 NUP58[0-1824] NUP58[1823-2367] PABPC3 POTPABPC1 PABPC4L
## [55] PABPC5 PCSK5 PRIM2[0-1071] PRIM2[1070-1902] PRKACB PRKACG
## [61] PTGES2[0-1587] PTGES2[1586-2202] RAB8B RAB13 RAB18[0-855] RAB18[854-1815]
## [67] RAB2B RAB5A RAB5B RAB15 RALB EZR
## [73] EZR[0-1458] EZR[1457-3771] MSN RETREG3 RHOB RHOC
## [79] SLC44A2[0-2577] SLC44A2[2576-3657] SPART SRP72[0-2604] SRP72[2603-3417] STOM[0-1047]
## [85] STOM[1046-1800] STOML3 TIMM29 TLE4 TLE2 TLE2[0-1302]
## [91] TLE2[1301-3987] TMPRSS2 TOMM70 TOR1B WASHC4 WFS1[0-2346]
## [97] WFS1[2345-3216] YIF1B
## 411 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ADAM9 ... ZYG11B
## 411 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ADAM9 ADAM9[0-3120] ADAM9[3119-3927] ADAMTS1 AES AGPS AKAP8 AKAP8L ... ZYG11B
\end{verbatim}
\begin{alltt}
\hlcom{# This includes paralogs, recombinations found by DGINN }
......@@ -235,10 +223,8 @@ I will merge the 2 tables.
\hlstd{tab[(tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlstd{F,}\hlstr{"Gene.name"}\hlstd{]}
\end{alltt}
\begin{verbatim}
## [1] "ADCK4" "ARL6IP6" "ATP5L" "C19orf52" "C1orf50" "ERO1LB"
## [7] "FAM134C" "FGFR1OP" "KIAA1033" "MFGE8" "NUPL1" "SIGMAR1"
## [13] "SPG20" "TCEB1" "TCEB2" "TOMM70A" "USP13" "VIMP"
## [19] "WHSC1"
## [1] "ADCK4" "ARL6IP6" "ATP5L" "C19orf52" "C1orf50" "ERO1LB" "FAM134C" "FGFR1OP" "KIAA1033" "MFGE8" "NUPL1"
## [12] "SIGMAR1" "SPG20" "TCEB1" "TCEB2" "TOMM70A" "USP13" "VIMP" "WHSC1"
\end{verbatim}
\begin{alltt}
\hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"Name"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{,} \hlstr{"GeneSize"}\hlstd{,} \hlstr{"dginn-primate_NbSpecies"}\hlstd{,} \hlstr{"dginn-primate_omegaM0Bpp"}\hlstd{,}
......@@ -496,34 +482,25 @@ Genes under positive selection for at least 4 methods.
\hlstd{tab}\hlopt{$}\hlstd{Gene.name[dginnfulltmp}\hlopt{>=}\hlnum{4} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F]}
\end{alltt}
\begin{verbatim}
## [1] "ACADM" "BCS1L" "BRD4" "CDK5RAP2" "CEP135" "CEP68"
## [7] "CLIP4" "DNMT1" "DPH5" "EMC1" "FYCO1" "GCC2"
## [13] "GGH" "GHITM" "GIGYF2" "GLA" "GOLGA7" "HECTD1"
## [19] "IDE" "ITGB1" "LARP1" "LARP4B" "LMAN2" "MARK1"
## [25] "MIPOL1" "MPHOSPH10" "MYCBP2" "NDUFAF2" "NDUFB9" "PCNT"
## [31] "POLA1" "PRIM2" "PRKAR2A" "PVR" "REEP6" "RIPK1"
## [37] "SAAL1" "SEPSECS" "SIRT5" "SLC25A21" "SLC27A2" "TMEM39B"
## [43] "TOR1AIP1" "TUBGCP2" "UBAP2" "UGGT2" "VPS39" "ZNF318"
## [1] "ACADM" "BCS1L" "BRD4" "CDK5RAP2" "CEP135" "CEP68" "CLIP4" "DNMT1" "DPH5" "EMC1"
## [11] "FYCO1" "GCC2" "GGH" "GHITM" "GIGYF2" "GLA" "GOLGA7" "HECTD1" "IDE" "ITGB1"
## [21] "LARP1" "LARP4B" "LMAN2" "MARK1" "MIPOL1" "MPHOSPH10" "MYCBP2" "NDUFAF2" "NDUFB9" "PCNT"
## [31] "POLA1" "PRIM2" "PRKAR2A" "PVR" "REEP6" "RIPK1" "SAAL1" "SEPSECS" "SIRT5" "SLC25A21"
## [41] "SLC27A2" "TMEM39B" "TOR1AIP1" "TUBGCP2" "UBAP2" "UGGT2" "VPS39" "ZNF318"
\end{verbatim}
\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name[dginnfulltmp}\hlopt{>=}\hlnum{3} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F]}
\end{alltt}
\begin{verbatim}
## [1] "ACADM" "ADAM9" "AP2A2" "ATE1" "BCS1L" "BRD4"
## [7] "BZW2" "CDK5RAP2" "CEP135" "CEP68" "CLIP4" "CNTRL"
## [13] "DNMT1" "DPH5" "EDEM3" "EIF4E2" "EMC1" "EXOSC2"
## [19] "FYCO1" "GCC2" "GGH" "GHITM" "GIGYF2" "GLA"
## [25] "GOLGA7" "GOLGB1" "GORASP1" "HDAC2" "HECTD1" "HS6ST2"
## [31] "IDE" "ITGB1" "LARP1" "LARP4B" "LARP7" "LMAN2"
## [37] "MARK1" "MDN1" "MIPOL1" "MOV10" "MPHOSPH10" "MRPS5"
## [43] "MYCBP2" "NAT14" "NDUFAF2" "NDUFB9" "NGLY1" "NPC2"
## [49] "PCNT" "PITRM1" "PLAT" "PLOD2" "PMPCB" "POLA1"
## [55] "POR" "PRIM2" "PRKAR2A" "PTBP2" "PVR" "RAB14"
## [61] "RAB1A" "RAB2A" "RAP1GDS1" "RBX1" "REEP6" "RIPK1"
## [67] "RPL36" "SAAL1" "SCCPDH" "SEPSECS" "SIRT5" "SLC25A21"
## [73] "SLC27A2" "STOM" "TIMM8B" "TMEM39B" "TOR1AIP1" "TRIM59"
## [79] "TRMT1" "TUBGCP2" "UBAP2" "UGGT2" "USP54" "VPS39"
## [85] "ZNF318"
## [1] "ACADM" "ADAM9" "AP2A2" "ATE1" "BCS1L" "BRD4" "BZW2" "CDK5RAP2" "CEP135" "CEP68"
## [11] "CLIP4" "CNTRL" "DNMT1" "DPH5" "EDEM3" "EIF4E2" "EMC1" "EXOSC2" "FYCO1" "GCC2"
## [21] "GGH" "GHITM" "GIGYF2" "GLA" "GOLGA7" "GOLGB1" "GORASP1" "HDAC2" "HECTD1" "HS6ST2"
## [31] "IDE" "ITGB1" "LARP1" "LARP4B" "LARP7" "LMAN2" "MARK1" "MDN1" "MIPOL1" "MOV10"
## [41] "MPHOSPH10" "MRPS5" "MYCBP2" "NAT14" "NDUFAF2" "NDUFB9" "NGLY1" "NPC2" "PCNT" "PITRM1"
## [51] "PLAT" "PLOD2" "PMPCB" "POLA1" "POR" "PRIM2" "PRKAR2A" "PTBP2" "PVR" "RAB14"
## [61] "RAB1A" "RAB2A" "RAP1GDS1" "RBX1" "REEP6" "RIPK1" "RPL36" "SAAL1" "SCCPDH" "SEPSECS"
## [71] "SIRT5" "SLC25A21" "SLC27A2" "STOM" "TIMM8B" "TMEM39B" "TOR1AIP1" "TRIM59" "TRMT1" "TUBGCP2"
## [81] "UBAP2" "UGGT2" "USP54" "VPS39" "ZNF318"
\end{verbatim}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{tab[dginnfulltmp}\hlopt{>=}\hlnum{4} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F,}
......
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