Commit 4ee6d2bd authored by mcariou's avatar mcariou
Browse files

add sub table

parent e04625e1
......@@ -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$Gene.name`==F])
write.csv(tabloK, "primatesVbats_onlykrogan.csv", row.names=FALSE, quote=FALSE)
@
\end{document}
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tmp$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
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