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Commit 085822ae authored by mcariou's avatar mcariou
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add sub table2

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covid_comp_dataset.Rnw
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......@@ -234,7 +234,9 @@ write.csv(tablo, "primatesVbats.csv", row.names=FALSE, quote=FALSE)
@
Restreindre ce tableau aux gènes présent dans l'analyse de Krogan.
<<setup, include=FALSE, cache=FALSE, tidy=TRUE>>=
options(tidy=TRUE, width=70)
@
<<>>=
# Reading the Krogan table
tab<-read.delim(paste0(workdir,
......
covid_comp_dataset.pdf
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covid_comp_dataset.tex
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......@@ -643,39 +643,72 @@ Restreindre ce tableau aux gènes présent dans l'analyse de Krogan.
\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"
## [1] "PCNT" "PVR" "POLA1" "FASTKD5" "PRIM2"
## [6] "ITGB1" "CNTRL" "SIRT5" "CEP250" "MRPS5"
## [11] "CENPF" "TRMT1" "SAAL1" "CEP68" "NINL"
## [16] "AKAP9" "NDUFAF2" "GOLGB1" "UGGT2" "SEPSECS"
## [21] "ABCC1" "CDK5RAP2" "PDE4DIP" "ACADM" "PRRC2B"
## [26] "SLC25A21" "PUSL1" "NDUFB9" "TOR1AIP1" "MDN1"
## [31] "GCC2" "ERLEC1" "FYCO1" "GHITM" "GORASP1"
## [36] "USP54" "ATE1" "MRPS27" "VPS39" "CEP350"
## [41] "ALG11" "MPHOSPH10" "SLC27A2" "ALG8" "BCS1L"
## [46] "STOM" "NUP210" "GOLGA2" "EDEM3" "DCTPP1"
## [51] "GIGYF2" "UBAP2" "DDX21" "RAB18" "MARK1"
## [56] "PRIM1" "C19orf52" "ZNF318" "ALG5" "EXOSC3"
## [61] "UBXN8" "PABPC1" "LMAN2" "RIPK1" "JAKMIP1"
## [66] "TARS2" "NDUFAF1" "PCSK6" "ANO6" "SNIP1"
## [71] "DNMT1" "PRKAR2B" "PLEKHA5" "FKBP15" "KDELC2"
## [76] "FBN1" "NUP88" "ATP13A3" "TRIM59" "NPC2"
## [81] "MEPCE" "PLAT" "EXOSC8" "CEP135" "GCC1"
## [86] "MIPOL1" "YIF1A" "AASS" "GLA" "FAM162A"
## [91] "FBXL12" "EXOSC5" "NGDN" "ATP6AP1" "LARP7"
## [96] "SIL1" "NUP62" "NDFIP2" "COLGALT1" "ECSIT"
## [101] "EMC1" "AP3B1" "POLA2" "CLIP4" "SLU7"
## [106] "CLCC1" "ERO1LB" "ATP5L" "ERMP1" "HS6ST2"
## [111] "NUPL1" "EIF4H" "ZYG11B" "EXOSC2" "ADCK4"
## [116] "WFS1" "TAPT1" "SPG20" "NGLY1" "FAR2"
## [121] "CHMP2A" "NLRX1" "NUP214" "PIGO" "PITRM1"
## [126] "ATP1B1" "PPT1" "HYOU1" "TUBGCP2" "KDELC1"
## [131] "WHSC1" "GDF15" "NARS2" "AKAP8" "TBK1"
## [136] "BRD4" "GRIPAP1" "PRKAR2A" "MOGS" "SCAP"
## [141] "AATF" "BRD2" "FBN2" "AKAP8L" "OS9"
## [146] "SIGMAR1" "MTCH1" "LARP4B" "FAM134C" "ARL6IP6"
## [151] "RBM28" "MRPS2" "CEP112" "LARP1" "INHBE"
## [156] "AGPS" "MRPS25" "MTARC1" "F2RL1" "MFGE8"
## [161] "SLC9A3R1" "CWC27" "CYB5B" "MAP7D1" "IDE"
## [166] "PMPCA" "GGH" "QSOX2" "GNG5" "PKP2"
## [171] "PMPCB" "RRP9" "NIN" "CUL2" "ADAM9"
## [176] "TMEM39B" "RAB8A" "CYB5R3" "GPAA1" "TM2D3"
## [181] "COMT" "SLC30A9" "PLD3" "CHPF" "SRP19"
## [186] "FKBP7" "DDX10" "ATP6V1A" "AAR2" "VIMP"
## [191] "NAT14" "MYCBP2" "ERC1" "DCAF7" "FBLN5"
## [196] "CSDE1" "TCEB1" "RAB14" "BZW2" "VPS11"
## [201] "CIT" "SLC30A6" "DPY19L1" "RTN4" "AP2M1"
## [206] "RNF41" "TOR1A" "PSMD8" "SLC44A2" "MOV10"
## [211] "RAB10" "NEU1" "MIB1" "TYSND1" "USP13"
## [216] "ZC3H7A" "IMPDH2" "DNAJC11" "NEK9" "PLEKHF2"
## [221] "IL17RA" "GNB1" "GRPEL1" "ARF6" "FKBP10"
## [226] "PABPC4" "HMOX1" "FOXRED2" "NOL10" "SRP72"
## [231] "ZDHHC5" "PTGES2" "TMED5" "HOOK1" "POFUT1"
## [236] "SUN2" "ERP44" "PRKACA" "GOLGA3" "ADAMTS1"
## [241] "CSNK2B" "THTPA" "PIGS" "RBM41" "C1orf50"
## [246] "TMEM97" "RAB2A" "STC2" "SMOC1" "FAM98A"
## [251] "INTS4" "RAB7A" "HECTD1" "STOML2" "POR"
## [256] "CSNK2A2" "HS2ST1" "DCAKD" "SRP54" "SDF2"
## [261] "ZNF503" "SBNO1" "RAE1" "TUBGCP3" "UPF1"
## [266] "ERGIC1" "TLE1" "TOMM70A" "KIAA1033" "DPH5"
## [271] "UBAP2L" "CHPF2" "GFER" "TIMM8B" "RAB5C"
## [276] "GOLGA7" "TIMM10" "HSBP1" "BCKDK" "ACSL3"
## [281] "PDZD11" "GGCX" "RALA" "LOX" "TBKBP1"
## [286] "CCDC86" "NUP98" "SCCPDH" "SCARB1" "CRTC3"
## [291] "ETFA" "FGFR1OP" "SLC30A7" "HEATR3" "COL6A1"
## [296] "RDX" "G3BP1" "TCF12" "ZC3H18" "G3BP2"
## [301] "AP2A2" "PLOD2" "MARK2" "TIMM9" "TIMM10B"
## [306] "RHOA" "REEP5" "REEP6" "FAM8A1" "PPIL3"
## [311] "TLE3" "AES" "RAP1GDS1" "HDAC2" "GTF2F2"
## [316] "NUP54" "MAT2B" "TCEB2" "MARK3" "PTBP2"
## [321] "RPL36" "TBCA" "NUTF2" "EIF4E2" "GPX1"
## [326] "RAB1A" "DNAJC19" "RBX1" "CISD3" "NPTX1"
## [331] "BAG5" "ACAD9" "ACE2" "TMPRSS2"
\end{verbatim}
\begin{alltt}
......@@ -699,17 +732,19 @@ Restreindre ce tableau aux gènes présent dans l'analyse 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
## [1] COQ8B ELOC ERO1B MARC1 NSD2 NUP58 PCSK5 RETREG3
## [9] SPART TIMM29 TOMM70 WASHC4
## 442 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ... 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"
## [1] "ADCK4" "AES" "ARL6IP6" "ATP5L" "BCS1L" "C19orf52"
## [7] "C1orf50" "CYB5R3" "ERO1LB" "FAM134C" "FGFR1OP" "KIAA1033"
## [13] "MFGE8" "MTARC1" "NUPL1" "SIGMAR1" "SPG20" "TCEB1"
## [19] "TCEB2" "TOMM70A" "USP13" "VIMP" "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{)}
......
figure/mondrianbats-1.pdf
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figure/mondrianbats-2.pdf
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figure/subsetbats-1.pdf
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figure/subsetbats-2.pdf
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figure/subsetbats-3.pdf
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figure/tablo-1.pdf
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figure/unnamed-chunk-3-1.pdf
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