add sub table

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}

primatesVbats_onlykrogan.csv

+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