update dataset

batssup3.csv

 x
+ACAD9
 ACADM
+ACE2
+ADAM9
 AGPS
+AKAP9
+ATP6AP1
 CDK5RAP2
+CISD3
+COL6A1
 EDEM3
 ERGIC1
 GGH
@@ -13,13 +20,20 @@ IMPDH2
 INHBE
 ITGB1
 LMAN2
+MARK2
+MIPOL1
 MOV10
 NUP214
 POLA1
 PRIM1
+PUSL1
+RAB18
+RAP1GDS1
+SCCPDH
 SLC27A2
 SLC30A9
 SLC44A2
+SLC9A3R1
 TBK1
 TOR1AIP1
 VPS39

covid_comp_dataset.Rnw

@@ -29,7 +29,7 @@
 Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
 
 
-<<>>=
+<<eval=FALSE>>=
 workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"
 
 tab<-read.delim(paste0(workdir, 
@@ -38,6 +38,15 @@ dim(tab)
 @
 
 
+
+<<>>=
+workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"
+
+tab<-read.delim(paste0(workdir, 
+  "covid_comp/covid_comp_alldginn.txt"), h=T, sep="\t")
+dim(tab)
+@
+
 \section{Comparison of dataset}
 
 \subsection{Data}
@@ -173,25 +182,25 @@ for (p in 0:5){
 tmp<-tablo$`tmp$Gene.name`[tablo$nbats==0 & tablo$nprimates==1]
 text(-0.4,-1.2, "p=1/n=0", cex=0.6)
 text(seq(from=0.1, to=5.5, length.out = 18),-1.1, tmp[1:18], cex=0.4)
-text(seq(from=0.1, to=3, length.out = length(tmp)-18),-1.3, tmp[19:length(tmp)], cex=0.4)
+text(seq(from=0.1, to=5.5, length.out = length(tmp)-18),-1.3, tmp[19:length(tmp)], cex=0.4)
 
 tmp<-tablo$`tmp$Gene.name`[tablo$nbats==1 & tablo$nprimates==1]
 text(-0.4,-1.7, "p=1/n=1", cex=0.6)
 text(seq(from=0.1, to=5.5, length.out = 18),-1.6, tmp[1:18], cex=0.4)
-text(seq(from=0.1, to=2, length.out = length(tmp)-18),-1.8, tmp[19:length(tmp)], cex=0.4)
+text(seq(from=0.1, to=4.5, length.out = length(tmp)-18),-1.8, tmp[19:length(tmp)], cex=0.4)
 
 
 tmp<-tablo$`tmp$Gene.name`[tablo$nbats==0 & tablo$nprimates==0]
-text(-0.4,-2.2, "p=0/n=0", cex=0.6)
+text(-0.4,-2.3, "p=0/n=0", cex=0.6)
 text(seq(from=0.1, to=5.5, length.out = 17),-2.1, tmp[1:17], cex=0.4)
-text(seq(from=0.1, to=4.4, length.out = length(tmp)-17),-2.3, tmp[18:length(tmp)], cex=0.4)
-
-tmp<-tablo$`tmp$Gene.name`[tablo$nbats==2 & tablo$nprimates==0]
-text(-0.4,-2.7, "p=0/n=2", cex=0.6)
-text(seq(from=0.1, to=5.5, length.out = 18),-2.6, tmp[1:18], cex=0.4)
-text(seq(from=0.1, to=1, length.out = length(tmp)-18),-2.8, tmp[19:length(tmp)], cex=0.4)
+text(seq(from=0.1, to=5.5, length.out = 17),-2.3, tmp[18:34], cex=0.4)
+text(seq(from=0.1, to=5.5, length.out = length(tmp)-34),-2.5, tmp[35:length(tmp)], cex=0.4)
 
 
+tmp<-tablo$`tmp$Gene.name`[tablo$nbats==2 & tablo$nprimates==0]
+text(-0.4,-2.9, "p=0/n=2", cex=0.6)
+text(seq(from=0.1, to=5.5, length.out = 18),-2.8, tmp[1:18], cex=0.4)
+text(seq(from=0.1, to=1, length.out = length(tmp)-18),-3.0, tmp[19:length(tmp)], cex=0.4)
 
 @
 
@@ -206,3 +215,6 @@ write.csv(tablo, "primatesVbats.csv", row.names=FALSE, quote=FALSE)
 
 \end{document}
 
+
+
+

primatesVbats.csv

@@ -2,21 +2,35 @@ 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
@@ -28,63 +42,94 @@ 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
+COQ8B,1,0
+CRTC3,1,2
+CSDE1,0,1
 CSNK2A2,0,0
 CSNK2B,0,1
+CUL2,2,0
 CWC27,1,2
-CYB5B,2,0
+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
+ELOC,2,0
 EMC1,2,5
 ERC1,1,1
 ERGIC1,4,0
 ERLEC1,0,2
 ERMP1,2,0
+ERO1B,0,4
 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
@@ -93,80 +138,140 @@ 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
+MARC1,0,0
+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
+NSD2,2,1
 NUP210,2,2
 NUP214,3,2
+NUP54,0,0
+NUP58,1,5
+NUP62,1,1
+NUP88,0,0
 NUP98,0,1
+NUTF2,0,1
 OS9,0,0
+PABPC1,0,0
 PABPC4,1,2
+PCNT,2,4
+PCSK5,1,0
+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
+RETREG3,0,1
+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
+SPART,1,0
+SRP19,0,1
 SRP54,0,0
 SRP72,1,1
 STC2,0,0
@@ -175,16 +280,24 @@ 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
+TIMM29,1,1
 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
+TOMM70,0,1
 TOR1A,1,1
 TOR1AIP1,5,5
 TRIM59,0,3
@@ -200,6 +313,10 @@ UPF1,0,0
 USP54,1,3
 VPS11,1,1
 VPS39,5,5
+WASHC4,2,2
+WFS1,2,2
+YIF1A,0,0
+ZC3H18,1,1
 ZC3H7A,1,1
 ZDHHC5,1,2
 ZNF318,0,5

primatessup3.csv

 x
 ACADM
+ACE2
+ADAM9
+AP2A2
+ATE1
+BRD4
+BZW2
 CDK5RAP2
 CEP135
 CEP68
 CLIP4
 CNTRL
+DNMT1
 DPH5
 EDEM3
+EIF4E2
 EMC1
+ERO1B
 EXOSC2
 FYCO1
+GCC2
 GGH
+GHITM
 GIGYF2
 GLA
 GOLGA7
 GOLGB1
 GORASP1
+HDAC2
 HECTD1
+HS6ST2
 IDE
 ITGB1
 LARP1
+LARP4B
 LARP7
 LMAN2
+MARK1
 MDN1
+MIPOL1
 MOV10
+MPHOSPH10
 MRPS5
 MYCBP2
+NAT14
+NDUFAF2
 NDUFB9
 NGLY1
 NPC2
+NUP58
+PCNT
 PITRM1
 PLAT
+PLOD2
+PMPCB
 POLA1
 POR
+PRIM2
 PRKAR2A
+PTBP2
+PVR
 RAB14
+RAB1A
 RAB2A
+RAP1GDS1
+RBX1
+REEP6
 RIPK1
+RPL36
 SAAL1
+SCCPDH
 SEPSECS
 SIRT5
 SLC25A21
@@ -45,6 +77,7 @@ SLC27A2
 STOM
 TIMM8B
 TMEM39B
+TMPRSS2
 TOR1AIP1
 TRIM59
 TRMT1