This function loads the pureCN-corrected
copy number data as generated by cnvKit call.
The data were accessed from /data/CCRBioinfo/projects/TargetOsteoDiscovery/report/summary.pureCN.cns.calls
on December 13, 2018.
target_cnv_calls()
Value
A GRanges object describing regions of copy number change with medata columns:
log2: log2 copy number
baf: average B-Allele-Frequency for the copy number region
cn: total integer copy number
cn1: integer copy number of allele 1
cn2: integer copy number of allele 2
depth: average depth of region
probes: from cnvKit, the number of bins
weight: from cnvKit
Examples
x = target_cnv_calls()#> #> #>head(x)#> GRanges object with 6 ranges and 10 metadata columns: #> seqnames ranges strand | sampleName #> <Rle> <IRanges> <Rle> | <character> #> [1] chr1 14362-3768985 * | 0A4HLD_Tumor #> [2] chr1 3773452-9787494 * | 0A4HLD_Tumor #> [3] chr1 9787494-12834483 * | 0A4HLD_Tumor #> [4] chr1 12834983-16160209 * | 0A4HLD_Tumor #> [5] chr1 16160978-40888454 * | 0A4HLD_Tumor #> [6] chr1 40888454-65829817 * | 0A4HLD_Tumor #> gene #> <character> #> [1] DDX11L1,WASH7P,WASH7P,WASH7P,MIR6859-4,MIR6859-3,MIR6859-1,MIR6859-2,OR4F5,LOC100133331,LINC00115,FAM41C,LOC100130417,SAMD11,SAMD11,NOC2L,NOC2L,KLHL17,PLEKHN1,PERM1,HES4,ISG15,AGRN,C1orf159,MIR200B,MIR200A,MIR429,TTLL10,TNFRSF18,TNFRSF4,SDF4,B3GALT6,FAM132A,UBE2J2,SCNN1D,ACAP3,ACAP3,MIR6726,PUSL1,PUSL1,CPSF3L,CPSF3L,CPSF3L,MIR6727,CPTP,TAS1R3,DVL1,DVL1,MIR6808,MXRA8,AURKAIP1,CCNL2,LOC148413,LOC148413,MRPL20,MRPL20,ANKRD65,TMEM88B,VWA1,ATAD3C,ATAD3B,ATAD3A,TMEM240,SSU72,MIB2,MMP23B,CDK11B,CDK11B,SLC35E2B,CDK11B,SLC35E2B,MMP23A,CDK11B,SLC35E2B,MMP23A,CDK11A,SLC35E2,NADK,GNB1,CALML6,TMEM52,CFAP74,GABRD,PRKCZ,PRKCZ,C1orf86,C1orf86,SKI,MORN1,MORN1,LOC100129534,RER1,RER1,PEX10,PEX10,PLCH2,PANK4,HES5,LOC115110,LOC115110,TNFRSF14,TNFRSF14,FAM213B,MMEL1,ACTRT2,LINC00982,PRDM16,ARHGEF16,MEGF6,MEGF6,MIR551A,TPRG1L,WRAP73,TP73,TP73-AS1,CCDC27,SMIM1,LRRC47,CEP104 #> [2] CEP104,DFFB,C1orf174,LINC01134,AJAP1,NPHP4,NPHP4,KCNAB2,KCNAB2,CHD5,RPL22,RNF207,ICMT,HES3,GPR153,ACOT7,HES2,ESPN,TNFRSF25,TNFRSF25,PLEKHG5,PLEKHG5,NOL9,TAS1R1,ZBTB48,KLHL21,PHF13,THAP3,THAP3,DNAJC11,DNAJC11,CAMTA1,VAMP3,PER3,UTS2,TNFRSF9,PARK7,ERRFI1,SLC45A1,RERE,RERE,LOC102724552,ENO1,ENO1,MIR6728,CA6,SLC2A7,SLC2A5,GPR157,MIR34A,H6PD,SPSB1,SLC25A33,TMEM201,PIK3CD,PIK3CD,PIK3CD-AS1 #> [3] CLSTN1,CTNNBIP1,LZIC,NMNAT1,NMNAT1,MIR5697,RBP7,UBE4B,KIF1B,PGD,APITD1,APITD1-CORT,APITD1-CORT,CORT,DFFA,PEX14,CASZ1,C1orf127,TARDBP,MASP2,SRM,EXOSC10,MTOR,MTOR,MTOR-AS1,ANGPTL7,UBIAD1,PTCHD2,FBXO2,FBXO2,FBXO44,FBXO44,FBXO6,MAD2L2,DRAXIN,AGTRAP,MTHFR,MTHFR,CLCN6,CLCN6,CLCN6,NPPA-AS1,NPPA-AS1,NPPA,NPPB,KIAA2013,PLOD1,MFN2,MIIP,TNFRSF8,MIR7846,TNFRSF1B,TNFRSF1B,VPS13D,DHRS3,DHRS3,MIR6730,AADACL4,AADACL3,C1orf158 #> [4] PRAMEF12,PRAMEF1,PRAMEF11,HNRNPCL4,HNRNPCL3,HNRNPCL1,HNRNPCL1,PRAMEF2,PRAMEF4,PRAMEF6,LOC101929983,PRAMEF9,LOC391003,PRAMEF22,HNRNPCL2,PRAMEF16,PRAMEF17,LOC400736,PRAMEF14,PRAMEF17,PDPN,PRDM2,KAZN,TMEM51-AS1,TMEM51,FHAD1,EFHD2,CTRC,CELA2A,CELA2B,CASP9,DNAJC16,DNAJC16,AGMAT,AGMAT,DDI2,DDI2,RSC1A1,RSC1A1,PLEKHM2,SLC25A34,TMEM82,FBLIM1,UQCRHL #> [5] FLJ37453,FLJ37453,SPEN,SPEN,MIR5096,ZBTB17,C1orf64,HSPB7,CLCNKA,CLCNKB,FAM131C,EPHA2,ARHGEF19,RSG1,FBXO42,SZRD1,SPATA21,NECAP2,CROCCP3,NBPF1,CROCCP2,MST1P2,ESPNP,MST1L,CROCC,MFAP2,ATP13A2,SDHB,PADI2,PADI1,PADI3,PADI4,PADI6,RCC2,ARHGEF10L,ACTL8,IGSF21,KLHDC7A,PAX7,TAS1R2,ALDH4A1,ALDH4A1,MIR4695,IFFO2,UBR4,EMC1,MRTO4,AKR7L,AKR7A3,AKR7A2,PQLC2,CAPZB,MINOS1,MINOS1-NBL1,MINOS1,MINOS1-NBL1,RPS14P3,MINOS1-NBL1,RPS14P3,NBL1,NBL1,HTR6,TMCO4,RNF186,OTUD3,PLA2G2E,PLA2G2A,PLA2G5,PLA2G2D,PLA2G2F,PLA2G2C,UBXN10-AS1,UBXN10,UBXN10,VWA5B1,CAMK2N1,MUL1,FAM43B,CDA,PINK1,MIR6084,PINK1-AS,PINK1-AS,DDOST,DDOST,KIF17,SH2D5,HP1BP3,EIF4G3,ECE1,NBPF3,ALPL,RAP1GAP,USP48,LDLRAD2,LDLRAD2,HSPG2,HSPG2,CELA3B,CELA3A,LINC00339,CDC42,WNT4,ZBTB40,EPHA8,C1QA,C1QC,C1QB,EPHB2,MIR4684,MIR4253,KDM1A,LUZP1,HTR1D,HNRNPR,ZNF436,ZNF436,ZNF436-AS1,ZNF436-AS1,TCEA3,ASAP3,E2F2,E2F2,LOC101928163,ID3,MDS2,RPL11,TCEB3,TCEB3,TCEB3-AS1,PITHD1,LYPLA2,GALE,HMGCL,FUCA1,CNR2,PNRC2,SRSF10,MYOM3,IL22RA1,IFNLR1,LOC284632,GRHL3,STPG1,NIPAL3,RCAN3,NCMAP,SRRM1,CLIC4,RUNX3,RUNX3,MIR6731,SYF2,RSRP1,RHD,TMEM50A,TMEM50A,RHCE,RHCE,TMEM57,LDLRAP1,MAN1C1,SEPN1,MTFR1L,LOC646471,MTFR1L,MTFR1L,AUNIP,AUNIP,PAQR7,STMN1,STMN1,MIR3917,PAFAH2,EXTL1,SLC30A2,TRIM63,PDIK1L,FAM110D,ZNF593,CNKSR1,CATSPER4,CEP85,SH3BGRL3,UBXN11,UBXN11,CD52,CD52,AIM1L,ZNF683,LIN28A,DHDDS,HMGN2,RPS6KA1,ARID1A,PIGV,ZDHHC18,SFN,GPN2,GPATCH3,NR0B2,NUDC,KDF1,TRNP1,FAM46B,SLC9A1,WDTC1,TMEM222,SYTL1,MAP3K6,FCN3,CD164L2,GPR3,WASF2,AHDC1,FGR,IFI6,FAM76A,STX12,PPP1R8,PPP1R8,SCARNA1,THEMIS2,RPA2,SMPDL3B,XKR8,EYA3,PTAFR,DNAJC8,ATPIF1,SESN2,MED18,PHACTR4,SNHG3,RCC1,SNORA73B,RCC1,SNORA73B,TRNAU1AP,TRNAU1AP,SNHG12,SNHG12,SNORD99,SNORA61,SNORA44,SNORA16A,RAB42,TAF12,GMEB1,YTHDF2,OPRD1,EPB41,TMEM200B,SRSF4,MECR,PTPRU,MATN1,MATN1,MATN1-AS1,LAPTM5,SDC3,PUM1,PUM1,SNORD103A,SNORD103B,SNORD103A,SNORD103B,SNORD85,NKAIN1,SNRNP40,ZCCHC17,FABP3,SERINC2,LINC01226,TINAGL1,HCRTR1,PEF1,COL16A1,ADGRB2,SPOCD1,PTP4A2,KHDRBS1,TMEM39B,KPNA6,TXLNA,CCDC28B,IQCC,DCDC2B,DCDC2B,TMEM234,TMEM234,EIF3I,MTMR9LP,FAM167B,LCK,HDAC1,MARCKSL1,TSSK3,BSDC1,ZBTB8B,ZBTB8A,ZBTB8OS,RBBP4,RBBP4,SYNC,SYNC,KIAA1522,YARS,YARS,S100PBP,S100PBP,FNDC5,HPCA,HPCA,TMEM54,TMEM54,RNF19B,AK2,AZIN2,TRIM62,ZNF362,PHC2,PHC2,MIR3605,PHC2,MIR3605,LOC101929464,LOC101929464,ZSCAN20,CSMD2,CSMD2,HMGB4,C1orf94,GJB5,GJB4,GJB3,GJA4,SMIM12,DLGAP3,ZMYM6,ZMYM1,SFPQ,ZMYM4,KIAA0319L,NCDN,TFAP2E,PSMB2,C1orf216,CLSPN,AGO4,AGO1,AGO3,TEKT2,ADPRHL2,COL8A2,TRAPPC3,MAP7D1,THRAP3,SH3D21,EVA1B,STK40,LSM10,OSCP1,MRPS15,CSF3R,GRIK3,ZC3H12A,MEAF6,MEAF6,MIR5581,SNIP1,DNALI1,DNALI1,GNL2,GNL2,RSPO1,C1orf109,CDCA8,EPHA10,MANEAL,YRDC,YRDC,C1orf122,C1orf122,MTF1,INPP5B,SF3A3,FHL3,UTP11L,POU3F1,RRAGC,MYCBP,GJA9-MYCBP,GJA9-MYCBP,GJA9,RHBDL2,AKIRIN1,NDUFS5,MACF1,MACF1,KIAA0754,BMP8A,BMP8A,PPIEL,PPIEL,PABPC4,PABPC4,LOC101929516,PABPC4,LOC101929516,SNORA55,HEYL,NT5C1A,HPCAL4,PPIE,PPIE,BMP8B,BMP8B,BMP8B,OXCT2,TRIT1,MYCL,MFSD2A,CAP1,PPT1,RLF,TMCO2,ZMPSTE24,COL9A2,SMAP2 #> [6] SMAP2,ZFP69B,ZFP69,EXO5,ZNF684,RIMS3,NFYC-AS1,NFYC-AS1,NFYC,NFYC,NFYC,MIR30E,NFYC,MIR30E,MIR30C1,KCNQ4,CITED4,CTPS1,SLFNL1-AS1,SLFNL1,SCMH1,EDN2,HIVEP3,GUCA2B,GUCA2A,FOXJ3,RIMKLA,ZMYND12,PPCS,CCDC30,PPIH,YBX1,CLDN19,P3H1,C1orf50,CCDC23,CCDC23,ERMAP,ERMAP,ZNF691,SLC2A1,SLC2A1,SLC2A1-AS1,FAM183A,EBNA1BP2,EBNA1BP2,MIR6733,EBNA1BP2,MIR6733,CFAP57,CFAP57,TMEM125,C1orf210,TIE1,MPL,CDC20,ELOVL1,ELOVL1,MIR6734,MED8,SZT2,HYI,PTPRF,KDM4A,KDM4A,KDM4A-AS1,ST3GAL3,LOC101929592,ST3GAL3,LOC101929592,MIR6079,ARTN,IPO13,DPH2,ATP6V0B,B4GALT2,CCDC24,CCDC24,SLC6A9,SLC6A9,KLF17,DMAP1,ERI3,ERI3,ERI3-IT1,RNF220,TMEM53,C1orf228,KIF2C,RPS8,RPS8,SNORD55,SNORD46,SNORD38A,SNORD38B,BEST4,PLK3,PLK3,TCTEX1D4,TCTEX1D4,BTBD19,PTCH2,EIF2B3,HECTD3,UROD,ZSWIM5,LINC01144,HPDL,MUTYH,MUTYH,TOE1,TOE1,TOE1,TESK2,TESK2,CCDC163P,MMACHC,MMACHC,PRDX1,PRDX1,AKR1A1,NASP,CCDC17,GPBP1L1,GPBP1L1,RPS15AP10,TMEM69,IPP,MAST2,PIK3R3,TSPAN1,POMGNT1,POMGNT1,LURAP1,LURAP1,RAD54L,RAD54L,LRRC41,LRRC41,UQCRH,NSUN4,FAAH,DMBX1,MKNK1-AS1,KNCN,MKNK1,MOB3C,ATPAF1,TEX38,EFCAB14-AS1,EFCAB14,EFCAB14,CYP4B1,CYP4Z2P,CYP4A11,CYP4X1,CYP4Z1,CYP4A22,PDZK1IP1,TAL1,STIL,CMPK1,LINC01389,FOXE3,FOXD2-AS1,FOXD2,SLC5A9,SPATA6,AGBL4,AGBL4,BEND5,ELAVL4,DMRTA2,FAF1,CDKN2C,C1orf185,RNF11,TTC39A,EPS15,OSBPL9,OSBPL9,NRD1,NRD1,NRD1,MIR761,RAB3B,TXNDC12,TXNDC12,KTI12,BTF3L4,ZFYVE9,CC2D1B,ORC1,PRPF38A,ZCCHC11,GPX7,FAM159A,COA7,ZYG11B,ZYG11A,ECHDC2,SCP2,PODN,SLC1A7,CPT2,C1orf123,MAGOH,LRP8,SLC25A3P1,DMRTB1,GLIS1,NDC1,YIPF1,DIO1,HSPB11,LRRC42,LDLRAD1,TMEM59,TCEANC2,MIR4781,CDCP2,CYB5RL,MRPL37,SSBP3,ACOT11,ACOT11,FAM151A,MROH7,MROH7-TTC4,MROH7-TTC4,TTC4,PARS2,TTC22,C1orf177,DHCR24,TMEM61,BSND,PCSK9,USP24,PPAP2B,PRKAA2,C1orf168,C8A,C8B,DAB1,OMA1,TACSTD2,MYSM1,JUN,HSD52,FGGY,FGGY,MIR4711,HOOK1,CYP2J2,C1orf87,NFIA,NFIA,NFIA-AS1,TM2D1,INADL,L1TD1,KANK4,USP1,DOCK7,DOCK7,ANGPTL3,ATG4C,FOXD3-AS1,FOXD3,FOXD3,ALG6,ITGB3BP,EFCAB7,EFCAB7,DLEU2L,PGM1,ROR1,UBE2U,CACHD1,CACHD1,MIR4794,RAVER2,JAK1,MIR101-1,AK4,DNAJC6 #> log2 baf cn cn1 cn2 depth probes #> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> #> [1] 0.759969 0.183258 3 3 0 90.2017 1019 #> [2] 1.131320 0.138159 4 4 0 107.5660 692 #> [3] 0.861385 0.109810 4 3 1 133.8180 734 #> [4] 1.424660 0.140513 5 5 0 159.1440 315 #> [5] 0.938908 0.144970 4 3 1 124.7990 4746 #> [6] 0.607871 0.216599 3 2 1 96.8659 2978 #> weight #> <numeric> #> [1] 289.321 #> [2] 219.499 #> [3] 225.408 #> [4] 101.239 #> [5] 1439.040 #> [6] 968.125 #> ------- #> seqinfo: 24 sequences from an unspecified genome; no seqlengthscolnames(x)#> NULL# Make a plot of log2 vs BAF for TP53 gene if (FALSE) { library(GenomicRanges) library(TxDb.Hsapiens.UCSC.hg19.knownGene) glocs = genes(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) library(AnnotationDbi) glocs$symbol = unlist(AnnotationDbi::select(org.Hs.eg.db, columns = "SYMBOL", keytype = "ENTREZID", keys = glocs$gene_id)$SYMBOL) glocs = glocs[!is.na(glocs$symbol)] tp53_regions = subsetByOverlaps(x, glocs[glocs$symbol=='TP53']) plot(tp53_regions$log2, tp53_regions$baf) }
