diff --git a/covid_comp_dataset.Rnw b/covid_comp_dataset.Rnw
index 50497236412da61b5c6d1708b81c25960ec24246..157f677a86e2323ea591bc65a415e1a9fbbc98b3 100644
--- a/covid_comp_dataset.Rnw
+++ b/covid_comp_dataset.Rnw
@@ -233,6 +233,42 @@ write.csv(tablo[tablo$nprimates>=3,"tmp$Gene.name"], "primatessup3.csv", row.nam
write.csv(tablo, "primatesVbats.csv", row.names=FALSE, quote=FALSE)
@
+Restreindre ce tableau aux gènes présent dans l'analyse de Krogan.
+
+<<>>=
+# Reading the Krogan table
+tab<-read.delim(paste0(workdir,
+ "data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"),
+ fill=T, h=T, dec=",")
+dim(tab)
+
+#Formating the column Gene.name and changing one wierd name
+tab$Gene.name<-as.character(tab$Gene.name)
+tab$Gene.name[tab$PreyGene=="MTARC1"]<-"MTARC1"
+
+#Adding ACE2 and TMPRSS2
+krogan<-c(tab$Gene.name, "ACE2", "TMPRSS2")
+
+# The list
+length(krogan)
+krogan
+
+#In the table, I select line that match the krogan gene name liste
+tabloK<-tablo[tablo$`tmp$Gene.name` %in% krogan,]
+
+# How many gene lost?
+dim(tablo)
+dim(tabloK)
+
+# Les gènes perdus (dans le tableau mais pas dans la liste de Krogan)
+sort(tablo$`tmp$Gene.name`[tablo$`tmp$Gene.name` %in% krogan==F])
+
+# Les gènes de Krogan non présent dans cette liste
+sort(krogan[krogan %in% tablo$`tmp$Gene.name`==F])
+
+
+write.csv(tabloK, "primatesVbats_onlykrogan.csv", row.names=FALSE, quote=FALSE)
+@
\end{document}
diff --git a/covid_comp_dataset.pdf b/covid_comp_dataset.pdf
index 37591cdac73e60769156f51add05788c9a09e198..9e62965b4d1d683bf7642c49d32a27d61ec8d0de 100644
Binary files a/covid_comp_dataset.pdf and b/covid_comp_dataset.pdf differ
diff --git a/covid_comp_dataset.tex b/covid_comp_dataset.tex
index b32dd9a7f4693cbc036e5b2a7f54c75d1098b042..a5f59cfd989a107b6b8bee9889a8ba575754ef8c 100644
--- a/covid_comp_dataset.tex
+++ b/covid_comp_dataset.tex
@@ -233,30 +233,18 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
-## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
-## 6 ACADM 1 1 1
-## 7 ACE2 1 1 1
-## 109 GGH 1 1 1
-## 117 GOLGA7 1 1 1
-## 134 IDE 1 1 1
-## 139 ITGB1 1 1 1
-## 146 LMAN2 1 1 1
-## 212 POLA1 1 1 1
-## 263 SLC27A2 1 1 1
-## 301 TOR1AIP1 1 1 1
-## 314 VPS39 1 1 1
-## primate_dginn4
-## 6 1
-## 7 1
-## 109 1
-## 117 1
-## 134 1
-## 139 1
-## 146 1
-## 212 1
-## 263 1
-## 301 1
-## 314 1
+## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
+## 6 ACADM 1 1 1 1
+## 7 ACE2 1 1 1 1
+## 109 GGH 1 1 1 1
+## 117 GOLGA7 1 1 1 1
+## 134 IDE 1 1 1 1
+## 139 ITGB1 1 1 1 1
+## 146 LMAN2 1 1 1 1
+## 212 POLA1 1 1 1 1
+## 263 SLC27A2 1 1 1 1
+## 301 TOR1AIP1 1 1 1 1
+## 314 VPS39 1 1 1 1
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -269,44 +257,25 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
-## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
-## 6 ACADM 1 1 1
-## 7 ACE2 1 1 1
-## 9 ADAM9 1 1 0
-## 34 CDK5RAP2 1 1 0
-## 71 EDEM3 1 1 1
-## 109 GGH 1 1 1
-## 117 GOLGA7 1 1 1
-## 134 IDE 1 1 1
-## 139 ITGB1 1 1 1
-## 146 LMAN2 1 1 1
-## 157 MIPOL1 1 1 0
-## 159 MOV10 1 1 0
-## 212 POLA1 1 1 1
-## 239 RAP1GDS1 1 1 1
-## 257 SCCPDH 1 1 0
-## 263 SLC27A2 1 1 1
-## 301 TOR1AIP1 1 1 1
-## 314 VPS39 1 1 1
-## primate_dginn4
-## 6 1
-## 7 1
-## 9 0
-## 34 1
-## 71 0
-## 109 1
-## 117 1
-## 134 1
-## 139 1
-## 146 1
-## 157 1
-## 159 0
-## 212 1
-## 239 0
-## 257 0
-## 263 1
-## 301 1
-## 314 1
+## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
+## 6 ACADM 1 1 1 1
+## 7 ACE2 1 1 1 1
+## 9 ADAM9 1 1 0 0
+## 34 CDK5RAP2 1 1 0 1
+## 71 EDEM3 1 1 1 0
+## 109 GGH 1 1 1 1
+## 117 GOLGA7 1 1 1 1
+## 134 IDE 1 1 1 1
+## 139 ITGB1 1 1 1 1
+## 146 LMAN2 1 1 1 1
+## 157 MIPOL1 1 1 0 1
+## 159 MOV10 1 1 0 0
+## 212 POLA1 1 1 1 1
+## 239 RAP1GDS1 1 1 1 0
+## 257 SCCPDH 1 1 0 0
+## 263 SLC27A2 1 1 1 1
+## 301 TOR1AIP1 1 1 1 1
+## 314 VPS39 1 1 1 1
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -322,88 +291,47 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
-## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
-## 31 BRD4 0 1 0
-## 34 CDK5RAP2 1 1 0
-## 37 CEP135 0 1 0
-## 40 CEP68 0 1 0
-## 47 CLIP4 0 1 0
-## 67 DNMT1 0 1 0
-## 68 DPH5 0 1 0
-## 75 EMC1 0 1 0
-## 80 ERO1B 0 1 0
-## 101 FYCO1 0 1 0
-## 105 GCC2 0 1 0
-## 110 GHITM 0 1 0
-## 111 GIGYF2 0 1 0
-## 112 GLA 0 1 0
-## 127 HECTD1 0 1 0
-## 143 LARP1 0 1 0
-## 144 LARP4B 0 1 0
-## 150 MARK1 0 1 0
-## 157 MIPOL1 1 1 0
-## 160 MPHOSPH10 0 1 0
-## 166 MYCBP2 0 1 0
-## 171 NDUFAF2 0 1 0
-## 172 NDUFB9 0 1 0
-## 187 NUP58 0 1 0
-## 195 PCNT 0 1 0
-## 218 PRIM2 0 1 0
-## 220 PRKAR2A 0 1 0
-## 227 PVR 0 1 0
-## 245 REEP6 0 1 0
-## 248 RIPK1 0 1 0
-## 253 SAAL1 0 1 0
-## 259 SEPSECS 0 1 0
-## 261 SIRT5 0 1 0
-## 262 SLC25A21 0 1 0
-## 296 TMEM39B 0 1 0
-## 298 TMPRSS2 0 1 0
-## 304 TUBGCP2 0 1 0
-## 307 UBAP2 0 1 0
-## 310 UGGT2 0 1 0
-## 321 ZNF318 0 1 0
-## primate_dginn4
-## 31 1
-## 34 1
-## 37 1
-## 40 1
-## 47 1
-## 67 1
-## 68 1
-## 75 1
-## 80 1
-## 101 1
-## 105 1
-## 110 1
-## 111 1
-## 112 1
-## 127 1
-## 143 1
-## 144 1
-## 150 1
-## 157 1
-## 160 1
-## 166 1
-## 171 1
-## 172 1
-## 187 1
-## 195 1
-## 218 1
-## 220 1
-## 227 1
-## 245 1
-## 248 1
-## 253 1
-## 259 1
-## 261 1
-## 262 1
-## 296 1
-## 298 1
-## 304 1
-## 307 1
-## 310 1
-## 321 1
+## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
+## 31 BRD4 0 1 0 1
+## 34 CDK5RAP2 1 1 0 1
+## 37 CEP135 0 1 0 1
+## 40 CEP68 0 1 0 1
+## 47 CLIP4 0 1 0 1
+## 67 DNMT1 0 1 0 1
+## 68 DPH5 0 1 0 1
+## 75 EMC1 0 1 0 1
+## 80 ERO1B 0 1 0 1
+## 101 FYCO1 0 1 0 1
+## 105 GCC2 0 1 0 1
+## 110 GHITM 0 1 0 1
+## 111 GIGYF2 0 1 0 1
+## 112 GLA 0 1 0 1
+## 127 HECTD1 0 1 0 1
+## 143 LARP1 0 1 0 1
+## 144 LARP4B 0 1 0 1
+## 150 MARK1 0 1 0 1
+## 157 MIPOL1 1 1 0 1
+## 160 MPHOSPH10 0 1 0 1
+## 166 MYCBP2 0 1 0 1
+## 171 NDUFAF2 0 1 0 1
+## 172 NDUFB9 0 1 0 1
+## 187 NUP58 0 1 0 1
+## 195 PCNT 0 1 0 1
+## 218 PRIM2 0 1 0 1
+## 220 PRKAR2A 0 1 0 1
+## 227 PVR 0 1 0 1
+## 245 REEP6 0 1 0 1
+## 248 RIPK1 0 1 0 1
+## 253 SAAL1 0 1 0 1
+## 259 SEPSECS 0 1 0 1
+## 261 SIRT5 0 1 0 1
+## 262 SLC25A21 0 1 0 1
+## 296 TMEM39B 0 1 0 1
+## 298 TMPRSS2 0 1 0 1
+## 304 TUBGCP2 0 1 0 1
+## 307 UBAP2 0 1 0 1
+## 310 UGGT2 0 1 0 1
+## 321 ZNF318 0 1 0 1
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -416,148 +344,77 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
-## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
-## 19 AP2A2 0 1 0
-## 23 ATE1 0 1 0
-## 31 BRD4 0 1 0
-## 32 BZW2 0 1 0
-## 37 CEP135 0 1 0
-## 40 CEP68 0 1 0
-## 47 CLIP4 0 1 0
-## 48 CNTRL 0 1 0
-## 67 DNMT1 0 1 0
-## 68 DPH5 0 1 0
-## 72 EIF4E2 0 1 0
-## 75 EMC1 0 1 0
-## 80 ERO1B 0 1 0
-## 83 EXOSC2 0 1 0
-## 101 FYCO1 0 1 0
-## 105 GCC2 0 1 0
-## 110 GHITM 0 1 0
-## 111 GIGYF2 0 1 0
-## 112 GLA 0 1 0
-## 118 GOLGB1 0 1 0
-## 119 GORASP1 0 1 0
-## 125 HDAC2 0 1 0
-## 127 HECTD1 0 1 0
-## 131 HS6ST2 0 1 0
-## 143 LARP1 0 1 0
-## 144 LARP4B 0 1 0
-## 145 LARP7 0 1 0
-## 150 MARK1 0 1 0
-## 154 MDN1 0 1 0
-## 160 MPHOSPH10 0 1 0
-## 164 MRPS5 0 1 0
-## 166 MYCBP2 0 1 0
-## 168 NAT14 0 1 0
-## 171 NDUFAF2 0 1 0
-## 172 NDUFB9 0 1 0
-## 176 NGLY1 0 1 0
-## 181 NPC2 0 1 0
-## 187 NUP58 0 1 0
-## 195 PCNT 0 1 0
-## 202 PITRM1 0 1 0
-## 204 PLAT 0 1 0
-## 208 PLOD2 0 1 0
-## 210 PMPCB 0 1 0
-## 214 POR 0 1 0
-## 218 PRIM2 0 1 0
-## 220 PRKAR2A 0 1 0
-## 224 PTBP2 0 1 0
-## 227 PVR 0 1 0
-## 230 RAB14 0 1 0
-## 232 RAB1A 0 1 0
-## 233 RAB2A 0 1 0
-## 242 RBX1 0 1 0
-## 245 REEP6 0 1 0
-## 248 RIPK1 0 1 0
-## 250 RPL36 0 1 0
-## 253 SAAL1 0 1 0
-## 259 SEPSECS 0 1 0
-## 261 SIRT5 0 1 0
-## 262 SLC25A21 0 1 0
-## 277 STOM 0 1 0
-## 290 TIMM8B 0 1 0
-## 296 TMEM39B 0 1 0
-## 298 TMPRSS2 0 1 0
-## 302 TRIM59 0 1 0
-## 303 TRMT1 0 1 0
-## 304 TUBGCP2 0 1 0
-## 307 UBAP2 0 1 0
-## 310 UGGT2 0 1 0
-## 312 USP54 0 1 0
-## 321 ZNF318 0 1 0
-## primate_dginn4
-## 19 0
-## 23 0
-## 31 1
-## 32 0
-## 37 1
-## 40 1
-## 47 1
-## 48 0
-## 67 1
-## 68 1
-## 72 0
-## 75 1
-## 80 1
-## 83 0
-## 101 1
-## 105 1
-## 110 1
-## 111 1
-## 112 1
-## 118 0
-## 119 0
-## 125 0
-## 127 1
-## 131 0
-## 143 1
-## 144 1
-## 145 0
-## 150 1
-## 154 0
-## 160 1
-## 164 0
-## 166 1
-## 168 0
-## 171 1
-## 172 1
-## 176 0
-## 181 0
-## 187 1
-## 195 1
-## 202 0
-## 204 0
-## 208 0
-## 210 0
-## 214 0
-## 218 1
-## 220 1
-## 224 0
-## 227 1
-## 230 0
-## 232 0
-## 233 0
-## 242 0
-## 245 1
-## 248 1
-## 250 0
-## 253 1
-## 259 1
-## 261 1
-## 262 1
-## 277 0
-## 290 0
-## 296 1
-## 298 1
-## 302 0
-## 303 0
-## 304 1
-## 307 1
-## 310 1
-## 312 0
-## 321 1
+## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
+## 19 AP2A2 0 1 0 0
+## 23 ATE1 0 1 0 0
+## 31 BRD4 0 1 0 1
+## 32 BZW2 0 1 0 0
+## 37 CEP135 0 1 0 1
+## 40 CEP68 0 1 0 1
+## 47 CLIP4 0 1 0 1
+## 48 CNTRL 0 1 0 0
+## 67 DNMT1 0 1 0 1
+## 68 DPH5 0 1 0 1
+## 72 EIF4E2 0 1 0 0
+## 75 EMC1 0 1 0 1
+## 80 ERO1B 0 1 0 1
+## 83 EXOSC2 0 1 0 0
+## 101 FYCO1 0 1 0 1
+## 105 GCC2 0 1 0 1
+## 110 GHITM 0 1 0 1
+## 111 GIGYF2 0 1 0 1
+## 112 GLA 0 1 0 1
+## 118 GOLGB1 0 1 0 0
+## 119 GORASP1 0 1 0 0
+## 125 HDAC2 0 1 0 0
+## 127 HECTD1 0 1 0 1
+## 131 HS6ST2 0 1 0 0
+## 143 LARP1 0 1 0 1
+## 144 LARP4B 0 1 0 1
+## 145 LARP7 0 1 0 0
+## 150 MARK1 0 1 0 1
+## 154 MDN1 0 1 0 0
+## 160 MPHOSPH10 0 1 0 1
+## 164 MRPS5 0 1 0 0
+## 166 MYCBP2 0 1 0 1
+## 168 NAT14 0 1 0 0
+## 171 NDUFAF2 0 1 0 1
+## 172 NDUFB9 0 1 0 1
+## 176 NGLY1 0 1 0 0
+## 181 NPC2 0 1 0 0
+## 187 NUP58 0 1 0 1
+## 195 PCNT 0 1 0 1
+## 202 PITRM1 0 1 0 0
+## 204 PLAT 0 1 0 0
+## 208 PLOD2 0 1 0 0
+## 210 PMPCB 0 1 0 0
+## 214 POR 0 1 0 0
+## 218 PRIM2 0 1 0 1
+## 220 PRKAR2A 0 1 0 1
+## 224 PTBP2 0 1 0 0
+## 227 PVR 0 1 0 1
+## 230 RAB14 0 1 0 0
+## 232 RAB1A 0 1 0 0
+## 233 RAB2A 0 1 0 0
+## 242 RBX1 0 1 0 0
+## 245 REEP6 0 1 0 1
+## 248 RIPK1 0 1 0 1
+## 250 RPL36 0 1 0 0
+## 253 SAAL1 0 1 0 1
+## 259 SEPSECS 0 1 0 1
+## 261 SIRT5 0 1 0 1
+## 262 SLC25A21 0 1 0 1
+## 277 STOM 0 1 0 0
+## 290 TIMM8B 0 1 0 0
+## 296 TMEM39B 0 1 0 1
+## 298 TMPRSS2 0 1 0 1
+## 302 TRIM59 0 1 0 0
+## 303 TRMT1 0 1 0 0
+## 304 TUBGCP2 0 1 0 1
+## 307 UBAP2 0 1 0 1
+## 310 UGGT2 0 1 0 1
+## 312 USP54 0 1 0 0
+## 321 ZNF318 0 1 0 1
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -573,30 +430,18 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{0}\hlstd{,]}
\end{alltt}
\begin{verbatim}
-## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
-## 14 AKAP9 1 0 1
-## 26 ATP6AP1 1 0 1
-## 44 CISD3 1 0 1
-## 71 EDEM3 1 1 1
-## 77 ERGIC1 1 0 1
-## 136 IMPDH2 1 0 1
-## 137 INHBE 1 0 1
-## 231 RAB18 1 0 1
-## 239 RAP1GDS1 1 1 1
-## 267 SLC44A2 1 0 1
-## 283 TBK1 1 0 1
-## primate_dginn4
-## 14 0
-## 26 0
-## 44 0
-## 71 0
-## 77 0
-## 136 0
-## 137 0
-## 231 0
-## 239 0
-## 267 0
-## 283 0
+## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
+## 14 AKAP9 1 0 1 0
+## 26 ATP6AP1 1 0 1 0
+## 44 CISD3 1 0 1 0
+## 71 EDEM3 1 1 1 0
+## 77 ERGIC1 1 0 1 0
+## 136 IMPDH2 1 0 1 0
+## 137 INHBE 1 0 1 0
+## 231 RAB18 1 0 1 0
+## 239 RAP1GDS1 1 1 1 0
+## 267 SLC44A2 1 0 1 0
+## 283 TBK1 1 0 1 0
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -609,48 +454,27 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{0}\hlstd{,]}
\end{alltt}
\begin{verbatim}
-## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4
-## 5 ACAD9 1 0 0
-## 11 AGPS 1 0 0
-## 14 AKAP9 1 0 1
-## 26 ATP6AP1 1 0 1
-## 44 CISD3 1 0 1
-## 49 COL6A1 1 0 0
-## 77 ERGIC1 1 0 1
-## 122 GRIPAP1 1 0 0
-## 123 GRPEL1 1 0 0
-## 136 IMPDH2 1 0 1
-## 137 INHBE 1 0 1
-## 151 MARK2 1 0 0
-## 185 NUP214 1 0 0
-## 217 PRIM1 1 0 0
-## 226 PUSL1 1 0 0
-## 231 RAB18 1 0 1
-## 266 SLC30A9 1 0 0
-## 267 SLC44A2 1 0 1
-## 268 SLC9A3R1 1 0 0
-## 283 TBK1 1 0 1
-## primate_dginn4
-## 5 0
-## 11 0
-## 14 0
-## 26 0
-## 44 0
-## 49 0
-## 77 0
-## 122 0
-## 123 0
-## 136 0
-## 137 0
-## 151 0
-## 185 0
-## 217 0
-## 226 0
-## 231 0
-## 266 0
-## 267 0
-## 268 0
-## 283 0
+## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
+## 5 ACAD9 1 0 0 0
+## 11 AGPS 1 0 0 0
+## 14 AKAP9 1 0 1 0
+## 26 ATP6AP1 1 0 1 0
+## 44 CISD3 1 0 1 0
+## 49 COL6A1 1 0 0 0
+## 77 ERGIC1 1 0 1 0
+## 122 GRIPAP1 1 0 0 0
+## 123 GRPEL1 1 0 0 0
+## 136 IMPDH2 1 0 1 0
+## 137 INHBE 1 0 1 0
+## 151 MARK2 1 0 0 0
+## 185 NUP214 1 0 0 0
+## 217 PRIM1 1 0 0 0
+## 226 PUSL1 1 0 0 0
+## 231 RAB18 1 0 1 0
+## 266 SLC30A9 1 0 0 0
+## 267 SLC44A2 1 0 1 0
+## 268 SLC9A3R1 1 0 0 0
+## 283 TBK1 1 0 1 0
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -787,6 +611,111 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\end{kframe}
\end{knitrout}
+Restreindre ce tableau aux gènes présent dans l'analyse de Krogan.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Reading the Krogan table}
+\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{"data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{dec}\hlstd{=}\hlstr{","}\hlstd{)}
+\hlkwd{dim}\hlstd{(tab)}
+\end{alltt}
+\begin{verbatim}
+## [1] 332 84
+\end{verbatim}
+\begin{alltt}
+\hlcom{#Formating the column Gene.name and changing one wierd name}
+\hlstd{tab}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{tab}\hlopt{$}\hlstd{Gene.name[tab}\hlopt{$}\hlstd{PreyGene}\hlopt{==}\hlstr{"MTARC1"}\hlstd{]}\hlkwb{<-}\hlstr{"MTARC1"}
+
+\hlcom{#Adding ACE2 and TMPRSS2}
+\hlstd{krogan}\hlkwb{<-}\hlkwd{c}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name,} \hlstr{"ACE2"}\hlstd{,} \hlstr{"TMPRSS2"}\hlstd{)}
+
+\hlcom{# The list}
+\hlkwd{length}\hlstd{(krogan)}
+\end{alltt}
+\begin{verbatim}
+## [1] 334
+\end{verbatim}
+\begin{alltt}
+\hlstd{krogan}
+\end{alltt}
+\begin{verbatim}
+## [1] "PCNT" "PVR" "POLA1" "FASTKD5" "PRIM2" "ITGB1" "CNTRL" "SIRT5" "CEP250" "MRPS5"
+## [11] "CENPF" "TRMT1" "SAAL1" "CEP68" "NINL" "AKAP9" "NDUFAF2" "GOLGB1" "UGGT2" "SEPSECS"
+## [21] "ABCC1" "CDK5RAP2" "PDE4DIP" "ACADM" "PRRC2B" "SLC25A21" "PUSL1" "NDUFB9" "TOR1AIP1" "MDN1"
+## [31] "GCC2" "ERLEC1" "FYCO1" "GHITM" "GORASP1" "USP54" "ATE1" "MRPS27" "VPS39" "CEP350"
+## [41] "ALG11" "MPHOSPH10" "SLC27A2" "ALG8" "BCS1L" "STOM" "NUP210" "GOLGA2" "EDEM3" "DCTPP1"
+## [51] "GIGYF2" "UBAP2" "DDX21" "RAB18" "MARK1" "PRIM1" "C19orf52" "ZNF318" "ALG5" "EXOSC3"
+## [61] "UBXN8" "PABPC1" "LMAN2" "RIPK1" "JAKMIP1" "TARS2" "NDUFAF1" "PCSK6" "ANO6" "SNIP1"
+## [71] "DNMT1" "PRKAR2B" "PLEKHA5" "FKBP15" "KDELC2" "FBN1" "NUP88" "ATP13A3" "TRIM59" "NPC2"
+## [81] "MEPCE" "PLAT" "EXOSC8" "CEP135" "GCC1" "MIPOL1" "YIF1A" "AASS" "GLA" "FAM162A"
+## [91] "FBXL12" "EXOSC5" "NGDN" "ATP6AP1" "LARP7" "SIL1" "NUP62" "NDFIP2" "COLGALT1" "ECSIT"
+## [101] "EMC1" "AP3B1" "POLA2" "CLIP4" "SLU7" "CLCC1" "ERO1LB" "ATP5L" "ERMP1" "HS6ST2"
+## [111] "NUPL1" "EIF4H" "ZYG11B" "EXOSC2" "ADCK4" "WFS1" "TAPT1" "SPG20" "NGLY1" "FAR2"
+## [121] "CHMP2A" "NLRX1" "NUP214" "PIGO" "PITRM1" "ATP1B1" "PPT1" "HYOU1" "TUBGCP2" "KDELC1"
+## [131] "WHSC1" "GDF15" "NARS2" "AKAP8" "TBK1" "BRD4" "GRIPAP1" "PRKAR2A" "MOGS" "SCAP"
+## [141] "AATF" "BRD2" "FBN2" "AKAP8L" "OS9" "SIGMAR1" "MTCH1" "LARP4B" "FAM134C" "ARL6IP6"
+## [151] "RBM28" "MRPS2" "CEP112" "LARP1" "INHBE" "AGPS" "MRPS25" "MTARC1" "F2RL1" "MFGE8"
+## [161] "SLC9A3R1" "CWC27" "CYB5B" "MAP7D1" "IDE" "PMPCA" "GGH" "QSOX2" "GNG5" "PKP2"
+## [171] "PMPCB" "RRP9" "NIN" "CUL2" "ADAM9" "TMEM39B" "RAB8A" "CYB5R3" "GPAA1" "TM2D3"
+## [181] "COMT" "SLC30A9" "PLD3" "CHPF" "SRP19" "FKBP7" "DDX10" "ATP6V1A" "AAR2" "VIMP"
+## [191] "NAT14" "MYCBP2" "ERC1" "DCAF7" "FBLN5" "CSDE1" "TCEB1" "RAB14" "BZW2" "VPS11"
+## [201] "CIT" "SLC30A6" "DPY19L1" "RTN4" "AP2M1" "RNF41" "TOR1A" "PSMD8" "SLC44A2" "MOV10"
+## [211] "RAB10" "NEU1" "MIB1" "TYSND1" "USP13" "ZC3H7A" "IMPDH2" "DNAJC11" "NEK9" "PLEKHF2"
+## [221] "IL17RA" "GNB1" "GRPEL1" "ARF6" "FKBP10" "PABPC4" "HMOX1" "FOXRED2" "NOL10" "SRP72"
+## [231] "ZDHHC5" "PTGES2" "TMED5" "HOOK1" "POFUT1" "SUN2" "ERP44" "PRKACA" "GOLGA3" "ADAMTS1"
+## [241] "CSNK2B" "THTPA" "PIGS" "RBM41" "C1orf50" "TMEM97" "RAB2A" "STC2" "SMOC1" "FAM98A"
+## [251] "INTS4" "RAB7A" "HECTD1" "STOML2" "POR" "CSNK2A2" "HS2ST1" "DCAKD" "SRP54" "SDF2"
+## [261] "ZNF503" "SBNO1" "RAE1" "TUBGCP3" "UPF1" "ERGIC1" "TLE1" "TOMM70A" "KIAA1033" "DPH5"
+## [271] "UBAP2L" "CHPF2" "GFER" "TIMM8B" "RAB5C" "GOLGA7" "TIMM10" "HSBP1" "BCKDK" "ACSL3"
+## [281] "PDZD11" "GGCX" "RALA" "LOX" "TBKBP1" "CCDC86" "NUP98" "SCCPDH" "SCARB1" "CRTC3"
+## [291] "ETFA" "FGFR1OP" "SLC30A7" "HEATR3" "COL6A1" "RDX" "G3BP1" "TCF12" "ZC3H18" "G3BP2"
+## [301] "AP2A2" "PLOD2" "MARK2" "TIMM9" "TIMM10B" "RHOA" "REEP5" "REEP6" "FAM8A1" "PPIL3"
+## [311] "TLE3" "AES" "RAP1GDS1" "HDAC2" "GTF2F2" "NUP54" "MAT2B" "TCEB2" "MARK3" "PTBP2"
+## [321] "RPL36" "TBCA" "NUTF2" "EIF4E2" "GPX1" "RAB1A" "DNAJC19" "RBX1" "CISD3" "NPTX1"
+## [331] "BAG5" "ACAD9" "ACE2" "TMPRSS2"
+\end{verbatim}
+\begin{alltt}
+\hlcom{#In the table, I select line that match the krogan gene name liste}
+\hlstd{tabloK}\hlkwb{<-}\hlstd{tablo[tablo}\hlopt{$}\hlstd{`tmp$Gene.name`} \hlopt{%in%} \hlstd{krogan,]}
+
+\hlcom{# How many gene lost?}
+\hlkwd{dim}\hlstd{(tablo)}
+\end{alltt}
+\begin{verbatim}
+## [1] 323 3
+\end{verbatim}
+\begin{alltt}
+\hlkwd{dim}\hlstd{(tabloK)}
+\end{alltt}
+\begin{verbatim}
+## [1] 311 3
+\end{verbatim}
+\begin{alltt}
+\hlcom{# Les gènes perdus (dans le tableau mais pas dans la liste de Krogan)}
+\hlkwd{sort}\hlstd{(tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{`tmp$Gene.name`} \hlopt{%in%} \hlstd{krogan}\hlopt{==}\hlstd{F])}
+\end{alltt}
+\begin{verbatim}
+## [1] COQ8B ELOC ERO1B MARC1 NSD2 NUP58 PCSK5 RETREG3 SPART TIMM29 TOMM70 WASHC4
+## 442 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ADAM9 ADAM9[0-2769] ADAM9[0-3120] ADAM9[2768-3030] ... ZYG11B
+\end{verbatim}
+\begin{alltt}
+\hlcom{# Les gènes de Krogan non présent dans cette liste}
+\hlkwd{sort}\hlstd{(krogan[krogan} \hlopt{%in%} \hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`}\hlopt{==}\hlstd{F])}
+\end{alltt}
+\begin{verbatim}
+## [1] "ADCK4" "AES" "ARL6IP6" "ATP5L" "BCS1L" "C19orf52" "C1orf50" "CYB5R3" "ERO1LB" "FAM134C" "FGFR1OP"
+## [12] "KIAA1033" "MFGE8" "MTARC1" "NUPL1" "SIGMAR1" "SPG20" "TCEB1" "TCEB2" "TOMM70A" "USP13" "VIMP"
+## [23] "WHSC1"
+\end{verbatim}
+\begin{alltt}
+\hlkwd{write.csv}\hlstd{(tabloK,} \hlstr{"primatesVbats_onlykrogan.csv"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
\end{document}
diff --git a/figure/mondrianbats-1.pdf b/figure/mondrianbats-1.pdf
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diff --git a/figure/mondrianbats-2.pdf b/figure/mondrianbats-2.pdf
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diff --git a/figure/subsetbats-1.pdf b/figure/subsetbats-1.pdf
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diff --git a/figure/subsetbats-2.pdf b/figure/subsetbats-2.pdf
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diff --git a/figure/subsetbats-3.pdf b/figure/subsetbats-3.pdf
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diff --git a/figure/tablo-1.pdf b/figure/tablo-1.pdf
index 108e006722ae5c7384879c3b274a1de78877d9f7..b9b9dcf90a67e8228b623b14c9fa1008483b4fcb 100644
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diff --git a/figure/unnamed-chunk-3-1.pdf b/figure/unnamed-chunk-3-1.pdf
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diff --git a/primatesVbats_onlykrogan.csv b/primatesVbats_onlykrogan.csv
new file mode 100644
index 0000000000000000000000000000000000000000..1872775fe38d4347754d5fa9dd0803536aff3901
--- /dev/null
+++ b/primatesVbats_onlykrogan.csv
@@ -0,0 +1,312 @@
+tmp$Gene.name,nbats,nprimates
+AAR2,0,0
+AASS,2,0
+AATF,0,1
+ABCC1,1,2
+ACAD9,3,1
+ACADM,4,5
+ACE2,5,5
+ACSL3,0,1
+ADAM9,3,3
+ADAMTS1,0,0
+AGPS,3,1
+AKAP8,0,0
+AKAP8L,0,1
+AKAP9,4,2
+ALG11,1,0
+ALG5,0,2
+ALG8,1,1
+ANO6,2,2
+AP2A2,1,3
+AP2M1,0,1
+AP3B1,1,1
+ARF6,0,0
+ATE1,0,3
+ATP13A3,0,2
+ATP1B1,2,0
+ATP6AP1,4,1
+ATP6V1A,1,1
+BAG5,0,0
+BCKDK,0,1
+BRD2,1,0
+BRD4,2,4
+BZW2,0,3
+CCDC86,0,0
+CDK5RAP2,3,5
+CENPF,1,2
+CEP112,1,1
+CEP135,0,4
+CEP250,1,2
+CEP350,0,2
+CEP68,1,5
+CHMP2A,2,1
+CHPF,0,2
+CHPF2,1,1
+CISD3,4,1
+CIT,1,2
+CLCC1,0,1
+CLIP4,2,4
+CNTRL,1,3
+COL6A1,3,2
+COLGALT1,2,1
+COMT,2,0
+CRTC3,1,2
+CSDE1,0,1
+CSNK2A2,0,0
+CSNK2B,0,1
+CUL2,2,0
+CWC27,1,2
+CYB5B,1,0
+DCAF7,0,1
+DCAKD,0,0
+DCTPP1,0,0
+DDX10,2,0
+DDX21,1,1
+DNAJC11,1,0
+DNAJC19,0,0
+DNMT1,1,5
+DPH5,0,4
+DPY19L1,0,0
+ECSIT,0,0
+EDEM3,5,3
+EIF4E2,1,3
+EIF4H,0,0
+EMC1,2,5
+ERC1,1,1
+ERGIC1,4,0
+ERLEC1,0,2
+ERMP1,2,0
+ERP44,1,0
+ETFA,0,0
+EXOSC2,0,3
+EXOSC3,1,0
+EXOSC5,0,0
+EXOSC8,0,0
+F2RL1,1,0
+FAM162A,0,0
+FAM8A1,1,1
+FAM98A,0,0
+FAR2,2,2
+FASTKD5,0,0
+FBLN5,1,1
+FBN1,2,2
+FBN2,2,2
+FBXL12,0,2
+FKBP10,1,0
+FKBP15,0,0
+FKBP7,0,2
+FOXRED2,2,0
+FYCO1,2,5
+G3BP1,1,1
+G3BP2,1,0
+GCC1,1,0
+GCC2,0,4
+GDF15,2,1
+GFER,0,1
+GGCX,1,0
+GGH,5,5
+GHITM,0,4
+GIGYF2,1,4
+GLA,1,4
+GNB1,0,1
+GNG5,0,1
+GOLGA2,2,2
+GOLGA3,0,1
+GOLGA7,5,5
+GOLGB1,2,3
+GORASP1,0,3
+GPAA1,2,0
+GPX1,0,1
+GRIPAP1,3,1
+GRPEL1,3,0
+GTF2F2,0,0
+HDAC2,0,3
+HEATR3,1,0
+HECTD1,2,5
+HMOX1,1,1
+HOOK1,0,0
+HS2ST1,2,0
+HS6ST2,0,3
+HSBP1,0,1
+HYOU1,2,1
+IDE,4,4
+IL17RA,1,0
+IMPDH2,4,1
+INHBE,5,0
+INTS4,1,0
+ITGB1,4,5
+JAKMIP1,2,0
+KDELC1,1,1
+KDELC2,0,0
+LARP1,1,4
+LARP4B,0,4
+LARP7,0,3
+LMAN2,4,4
+LOX,1,1
+MAP7D1,0,1
+MARK1,1,4
+MARK2,3,0
+MARK3,2,1
+MAT2B,0,0
+MDN1,2,3
+MEPCE,2,0
+MIB1,2,0
+MIPOL1,3,4
+MOGS,0,0
+MOV10,3,3
+MPHOSPH10,1,4
+MRPS2,0,1
+MRPS25,1,0
+MRPS27,1,2
+MRPS5,2,3
+MTCH1,1,0
+MYCBP2,2,5
+NARS2,1,1
+NAT14,0,3
+NDFIP2,0,1
+NDUFAF1,0,2
+NDUFAF2,0,5
+NDUFB9,0,4
+NEK9,2,0
+NEU1,2,0
+NGDN,0,0
+NGLY1,1,3
+NIN,1,0
+NINL,0,2
+NLRX1,1,2
+NOL10,1,1
+NPC2,0,3
+NPTX1,1,0
+NUP210,2,2
+NUP214,3,2
+NUP54,0,0
+NUP62,1,1
+NUP88,0,0
+NUP98,0,1
+NUTF2,0,1
+OS9,0,0
+PABPC1,0,0
+PABPC4,1,2
+PCNT,2,4
+PCSK6,2,0
+PDE4DIP,0,1
+PDZD11,0,1
+PIGO,0,1
+PIGS,0,0
+PITRM1,1,3
+PKP2,0,1
+PLAT,1,3
+PLD3,0,1
+PLEKHA5,0,0
+PLEKHF2,2,0
+PLOD2,1,3
+PMPCA,0,2
+PMPCB,2,3
+POFUT1,2,1
+POLA1,4,4
+POLA2,1,0
+POR,2,3
+PPIL3,0,1
+PPT1,1,0
+PRIM1,3,2
+PRIM2,0,5
+PRKACA,1,0
+PRKAR2A,1,4
+PRKAR2B,1,2
+PRRC2B,1,0
+PSMD8,2,1
+PTBP2,0,3
+PTGES2,2,1
+PUSL1,3,1
+PVR,2,5
+QSOX2,1,1
+RAB10,0,0
+RAB14,0,3
+RAB18,5,1
+RAB1A,0,3
+RAB2A,0,3
+RAB5C,0,2
+RAB7A,0,1
+RAB8A,1,0
+RAE1,1,1
+RALA,0,0
+RAP1GDS1,5,3
+RBM28,2,0
+RBM41,0,2
+RBX1,0,3
+RDX,2,0
+REEP5,0,0
+REEP6,0,5
+RHOA,0,0
+RIPK1,2,4
+RNF41,0,0
+RPL36,1,3
+RRP9,2,1
+RTN4,1,2
+SAAL1,1,4
+SBNO1,2,2
+SCAP,1,2
+SCARB1,2,2
+SCCPDH,3,3
+SDF2,0,0
+SEPSECS,2,5
+SIL1,1,0
+SIRT5,1,4
+SLC25A21,0,4
+SLC27A2,5,4
+SLC30A6,0,0
+SLC30A7,1,1
+SLC30A9,3,0
+SLC44A2,5,0
+SLC9A3R1,3,0
+SLU7,1,2
+SMOC1,0,2
+SNIP1,0,0
+SRP19,0,1
+SRP54,0,0
+SRP72,1,1
+STC2,0,0
+STOM,1,3
+STOML2,0,0
+SUN2,2,0
+TAPT1,1,2
+TARS2,0,1
+TBCA,2,1
+TBK1,5,2
+TBKBP1,0,2
+TCF12,0,1
+THTPA,0,0
+TIMM10,1,0
+TIMM10B,0,0
+TIMM8B,0,3
+TIMM9,0,0
+TLE1,2,1
+TLE3,0,1
+TM2D3,1,1
+TMED5,2,0
+TMEM39B,2,4
+TMEM97,0,1
+TMPRSS2,0,4
+TOR1A,1,1
+TOR1AIP1,5,5
+TRIM59,0,3
+TRMT1,1,3
+TUBGCP2,0,4
+TUBGCP3,2,1
+TYSND1,2,0
+UBAP2,0,4
+UBAP2L,1,1
+UBXN8,0,1
+UGGT2,1,4
+UPF1,0,0
+USP54,1,3
+VPS11,1,1
+VPS39,5,5
+WFS1,2,2
+YIF1A,0,0
+ZC3H18,1,1
+ZC3H7A,1,1
+ZDHHC5,1,2
+ZNF318,0,5
+ZNF503,0,1
+ZYG11B,0,2