I have a data set that is a GMT file:
SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM http://www.gsea-msigdb.org/gsea/msigdb/human/geneset/SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM ADGRV1 MAP3K7CL CLEC3B SLC1A3 STN1
LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_UP http://www.gsea-msigdb.org/gsea/msigdb/human/geneset/LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_UP RPLP0P11 PFN1P11 DSCAM-AS1 MT-TS2 FGB MT-TL2 PAX2 FOXB1 MAGEC2 SLC28A2 LINC02593 CPLX2 MGAT5B SBK2 LEMD1-DT ANK1 EVPLL TGM7 LCN10 ENSG00000262884 DISP3 SIAH3 IGSF23 RD3 MYOM3 MIR4664 NAT8L ALPL LINC01001 FOXI3 KCNH3 GRIN2B XKR7 CELSR3 CICP27 RASSF10 LINC02108 SKIDA1 STAG3L3 FAR2P1 LINC01224 ID1 WDR62 CCDC150 PLEKHG4B RBM25-AS1 STAG3L5P KIF18B ZDHHC8P1 DDX12P MKRN3 GOLGA2P5 TUBA5P ZNF114 LINC00319 MYBL2 UCA1 KSR2 CYSRT1 MIR1302-9HG HASPIN MKI67 CNGB1 MIR29B2CHG GGT2P CCNF SNORD86 LY6G5B FBN3 DUX4L27 RNFT2 ULBP3 MAP3K9 LINC01873 LINC01764 LINC00958 TROAP PALM3 PIF1 OCLNP1 P2RY2 GPAT4-AS1 RAP1GAP2 ENSG00000260874 KIF12 PAX8-AS1 FAM215B MT-TH PROX2 CLSPN LHX4 SULT1A3 DACT2 GPC1-AS1 LINC01609 HS6ST1P1 CIT ADGRL1-AS1 AFG3L1P DLX4 PLXNA4 TICRR PRPS1P2 RCOR2 JRK CLCNKA DNAH10OS PACSIN1 LINC01089 ESPL1 SPTBN5 MIR600HG BPTFP1 POMK NINL ADGRL1 RECQL4 WASH4P CLDN9 KIFC1 LINC00664 NECTIN1 ADRA1B SSUH2 LINC00265 ARHGEF34P OBSCN SPAG5 OVOL1 EIF3CL PBX2P1 KRT8P3 YWHAZP5 TUBAP2 H2BC12L AHCTF1P1 UBE2SP2 TUBBP1 PSMC1P1 RTN3P1 BANF1P3 HSP90AB3P SETP14 DGKZP1 PPP1R14BP3 VDAC2P5 UBQLN4P1 TLK2P1 PHC1P1 YTHDF2P1 RANP1 PFN1P1 ATF4P3 RALGAPA1P1 BRD7P2 HMGB1P6 RAMACL COX6A1P2 HMGB1P5 HNRNPA1P10 HNRNPA1P7 RNPS1P1 TPM3P5 HNRNPA3P6 SERBP1P5 HSPD1P1 DHFRP1 SRSF6P2 THAP12P7 RPSAP54 HSPB1P1 RPL6P27 PCBP2P2 PSMA6P1 HNRNPCP2 EIF4BP7 NPM1P7 FABP5P7 RPL26P30 YBX1P1 EIF4BP6 RANBP1P1 SUMO2P1 ATF4P4 RPS27AP5 XRCC6P2 EIF4HP1 EIF4A1P10 RPS7P10 TCEA1P2 GCSHP5 MTX1P1 TMEM183BP SNRPGP15 NPM1P27 CSNK2A3 RPS7P11 SRP9P1 GDI2P2 CHCHD2P9 PPIAP22 RPL3P2 RPL7AP30 EEF1A1P6 RPL4P4 PGAM4 RPL6P10 PDIA3P1 PABPC3 CEP170P1 EIF4EP2 RPLP0P9 FAM3C2P DNAJB6P1 RPL10P6 ARPC3P3 SERBP1P1 RPL10P9 ANXA2P2 ST13P6 RPS24P19 RPL22P1 H3-5 LINC02067 RPL23AP42 BZW1P2 MXRA7P1 RPS27AP16 EIF2S2P4 SUMO2P21 EIF1AXP1 MEMO1P1 RPL4P5 EEF1B2P3 RPL35P2 GMPSP1 ENSG00000244398 RPL24P4 EIF3LP2 PRR13P5 RPL7P9 ARMC10P1 SPCS2P4 RPSAP15 DSTNP3 RAB6D YWHAZP3
LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_DN http://www.gsea-msigdb.org/gsea/msigdb/human/geneset/LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_DN RPL7AP6 CACYBPP2 PTGES3P3 RPL15P3 HMGN2P5 BTF3L4P2 DYNC1I2P1 RAC1P2 FKBP1C EIF2S3B ENSG00000174977 RPL7P1 RPS3AP26 CDC42P6 RPL26P36 RPL18AP3 MORF4L1P1 RPL12P4 RPL26P19 ITGB1P1 RPL5P4 PDIA3P2 RPL10P16 RPL39P3 FTH1P2 TWF1P1 RPL3P4 RPS27AP11 RPS3AP21 TAGLN2P1 NDUFB4P12 RPL21P16 RPL41P1 RPL5P1 RAB6C RPS23P8 RPL13P12 EEF1B2P6 FTH1P10 RPS2P5 RAP1BL RPS3AP6 SEPTIN7P3 RPL17P36 RPL13AP5 RPL9P7 NAMPTP1 RPS13P2 ZC3H12A-DT PSD3 ST3GAL5 COL4A2-AS1 MANEA SLC18A2 VWA1 ROBO2 IFNGR1 ITPR2 PDLIM5 ASPH TPBG FCHO2 CNTNAP1 GRK3 EAF2 ITGB6 TNFAIP8 BTN3A3 SERPINB1 MAP3K4-AS1 STARD5 PRICKLE2 PRKACB RHOB TPST2 ADAM22 SLIT2 BHLHE41 LPXN MAFF ADAMTSL4 SMARCA2 ANKRD44 APOBEC3G CHN1 DYNLT3 WNT5A MSN NFATC2 NME5 HSD17B11 CDKN1A TMEM86A SLC16A3 IRF1 CAMK2D CAVIN1 C10orf55 MGLL HHIPL1 PSMB10 CAVIN3 DNAJB4 AMPD3 DERL3 BTN3A2 TSHZ1 SFXN3 ARL15 FZD1 PLEKHO2 UPP1 CTSL FAM171B A4GALT SEPTIN11 SPART CTBS B3GNT9 CISH TMEM98 HLA-K PDE5A RASSF4 ITM2B CALD1 FKBP5 IRS1 TRIM47 NIPAL2 PLS3 MTUS1 LDAF1 TIPARP RPS27L PREX2 SERPING1 STARD13 ANXA6 GPSM3 PLD1 CYP1B1 BTBD19 PRCD RECK TRIL RAB42 PLK3 WNT5B CYTOR RTN4RL2 DEPTOR CD40 HLA-J CYRIA IL6ST PLAU PPP3CC ELOVL4 AHR CHN2 GSDME IGDCC4 MARCHF3 ERAP2 C2 CDH2 CLIC4 NLRC5 CSPG4 SLPI MAP1LC3A PTEN RIPOR2 IFIT3 HBEGF MAN2A1 HLA-H P3H3 HLA-E SMOC2 ADORA2A KCNK6 MMRN2 SEMA3C EOGT KLRG1 RBPMS-AS1 BMERB1 ARRDC3 PDK4 IGFBP4 PTAFR TIMP2 MYH11 TRPS1 RARRES2 PDE7B SERPINB8 WFDC21P GPX8 CDK14 SATB2 PLOD2 SELENOP EVA1C CASP10 CORO1A-AS1 SBSPON MMP19 DSEL HLA-A CRISPLD2 DRAM1 NRROS WASF3 PYCARD LTBP2 FBLN5 KIF17 PYCARD-AS1 TNFAIP3 FLT3LG MAP1B ABCC3 LCN2 ICAM5 SNX10 ITGA2 GSDMC CMTM3 LMOD1 OGFRL1 IL15 TAP1 SH3BGRL RORA KLHDC1 HLA-DMB LACC1 SGPP1 DHRS3 SLC43A1 MAPK11 UBA7 ODAD2 TNFRSF11B INPP4B NLRC3 HCG4B PPM1L DUSP5 SEMA5B GLIPR2 SLC16A14 ABHD3 SCARF2 CHST2 PPP1R16B FAM43A SLC7A7 CRACR2A APOL4 SDC2 BNC1 CCDC152 FKBP14 PAMR1 CSGALNACT1 MATN3 PSMB8-AS1 SPRED1 RRAS SAMD5 IL7 ENSG00000225032 ALDH1A3-AS1 SLC2A13 SMIM3 CLVS1 POGLUT2 SCIMP LGALS9 FHL2 SULF2 AFAP1L1 SCN1B VSIR LINC00511 ARSI NRP2 ARHGAP10 AKR1C3 RAMP1 TLR3 SOD3 RAB8B SERPINB9 FAM89A TRABD2A FRMD3 STING1 CXCL3 EIF5A2 SOD2 DPYSL2 DOCK8 FAM78A RAB27B QPCT RRAGD TGFA LRP1 FHOD3 POU2F2 C1QTNF6 SLC31A2 SYDE1 CASC15 HLA-C DAPL1 LINC01140 EPSTI1 SIRPA OSTM1 DPP7 PHLDA1 SETD7 SLCO2A1 GAS6 FAM126A CORO1A RASGRP2 JAZF1 KCNS3 FTLP3 FAS LYSMD2 TNFRSF14 TNFRSF18 EXOC3L1 PLAT DTNA CHI3L1 NKX3-1 ATP2A3 EPS8 GAS6-AS1 GPR176 TTYH2 PPP2R2C ANOS1 ADGRB3 HCP5 CACNA2D4 JAK2 ADAMTSL2 LRCH2 GSPT2 HEG1 GAS6-DT CPP FAM13C RASIP1 DNAJC12 CXCL1 MMP14 ITPR1 CFB FSTL1 IL32 RGL1 SLC16A2 FTL CP KANK3 PDGFRL IFIT2 LRRC8C KCNK3 SP140 SLC1A1 SLITRK2 KLF6 GALNT18 NLRP1 MCC SERPINI1 PHLDB2 TRIM22 RAB3IL1 SAT1 PAG1 BEND6 TMEM154 CHST7 GPRASP1 CHRNA1 RGS7BP SLC7A2 SKAP2 TMEM150C ADGRE2 FAM81B ZCCHC24 LXN F2R TMEM273 TCIM COL12A1 TACC1 NAAA CHST11 CILP2 RUNX1 PYGO1 ADCY4 NPTX2 JAK3 ESR1 SH3RF3 PPP2R2B AMIGO2 LGALS1 NR3C1 CA2 PLA2R1 TENM3 TAGLN MRGPRF SLFN11 FXYD5 LRRC17 GPR137B LRRC32 TARID NTS SP6 EPAS1 GABRB3 SIRPB1 DGKI VWC2 GBP2 SLC16A6 GJB6 PXDNL VWA5A GSTM5 ARHGAP24 CARD6 DCHS1 RCAN2 BCL2 ELN SYNE1 MT-TM LPAR5 MN1 ITPRIP WDR17 NOD2 NPY1R FKBP7 PNMA2 C2CD4B DCHS1-AS1 LHFPL2 EFCC1 NBL1 CCN1 PLCL1 PODNL1 MT1G CFI FAM20A KITLG CARD16 TCF4 HOXC6 MRC2 C8orf88 MPP1 TSHZ2 TGFB1I1 THSD1 IGF1 STK17B ERO1B SNHG28 ALKAL2 ATP10D MRAP2 NR4A1 H19 PLPPR3 WSCD1 NAP1L3 DCHS2 PDE3B IL15RA ME1 KCTD12 FBXO32 STOM ELN-AS1 KCNK13 SNRPA1-DT STEAP2 CLIC2 KCNAB2 GULP1 MIR100HG CCDC69 TMEM47 SOCS2 ENSG00000253882 ATP1B2 PRKD1 OSBPL6 NEXN FGF13 ACP5 NRXN2 TNFRSF9 OLFM1 CD200 NPR3 IL4R PDZD4 ADM KCNA6 PAEP PI15 SCG5 CMAHP BMP6 SERPINA1 GNG11 RASA3 IL18 CAV1 TNFRSF11A CXCL17 PKIB GPR132 ZFPM2 DKK3 GUCY1A1 ELMO1 GRK5 PCK1 FST NR4A1AS TAFA2 SAMD9L CACNA1G ICAM4-AS1 CD38 IFI30 STAT4 SIDT1 ADAMTS7 CYP27A1 HSPA12B GAS1 MT1H SLC46A3 DOCK4 COL4A1 SNCAIP CCL20 SPHK1 THSD7B ANTXR1 MAN1C1 RHOBTB3 FCMR MCTP1 CCDC68 HSPB8 KCNA5 TG TBC1D4 HCAR2 STARD8 LDLRAD4 GHR FAM83B NKD2 FLT4 LGALS2 FMO3 HSPA7 GDNF SPOCK1 B2M KCNT2 HLA-DMA TNFSF10 GPR68 SGK1 HCST PCED1B MFNG PLA2G7 NFASC CPE MT2A C1R PLAAT4 NUDT10 ACSL5 PDE1B TIE1 RIMBP2 HP NLRC4 CEBPD SYCE1 CLIC6 SH2B3 HLA-B PITX2 PALLD CAVIN2 SECTM1 TRABD2B PDPN SLC47A1 SLC4A4 CYP7B1 EMP3 CHGB CYGB CCDC85A ADGRA2 MT1E PDZK1IP1 TLE4 DUSP2 HEYL LAMB1 LIPA ICAM1 DIRAS3 ALDH1A3 CPNE5 CALB2 PCOLCE2 CACNA1C ALPK2 DCLK1 TIMP3 BCL11B HTR2B ETS1 PDGFD SLC24A3 APOL1 RARB AXL MIAT APOL6 CCDC80 SULT1C4 COPZ2 NOTCH4 TSPAN5 CPNE8 LAG3 SPIB PDZRN4 UNC5C PTN THSD7A CNTN4 SELENOM SLC40A1 FNDC4 IL1RN AQP1 COL2A1 ENPEP JUNB ENSG00000258086 ZNF365 PROCR NECAB1 TLR6 SNCA PDE1A DPP4 IFI16 ADAMTSL1 FAT4 PEG3 SOCS3 GFRA1 NEFH PIK3AP1 PLAUR MEIS2 NR4A3 SFRP1 HLF VIM-AS1 LOX RFTN1 TESC TM6SF1 THY1-AS1 SERPINE2 SQOR AK5 DPYSL4 GRAP ADCYAP1R1 JAM2 GGTA1 BIRC3 SYPL2 ITGA5 SOX18 CYBRD1 CCDC102B ARHGAP20 STAMBPL1 ARHGAP30 ELL2 EMILIN2 PTPRE SLITRK4 CD274 HEY1 HS3ST3A1 IL18R1 MARCHF1 PRRG3 MAPRE2 COL8A2 SATB1 ADAM8 ATRNL1 C3 PLPP4 ADA2 SLC12A5-AS1 GLRX SLITRK5 SLC11A1 GTSF1 SRPX ENSG00000253837 VIM CELF2 THY1 C16orf89 CLDN11 GNB4 SCARF1 CX3CR1 GASK1B-AS1 PLXDC1 IRAG2 APOE CDC42EP5 CLEC11A ITIH3 FOXL1 PCSK6 GRIK3 WTAPP1 C2CD4C LZTS1 KCND3 TNFAIP8L3 TBXAS1 CD96 TIMP1 ABLIM3 ACTG2 CHSY3 C12orf60 JCAD PLVAP BEND4 CD74 STK32B PCYT1B RTN1 GADD45B ABI3BP DACT3 ARHGAP25 GLI1 PLA2G4C IL3RA RGS16 PLCB2 VWFP1 RAMP2 BMP2 KLF9 SH2D3C CD69 HNMT AOC3 CACNA2D1 LOXL2 RUNX2 NTRK2 ZFHX4 PSMB9 MAOB RCN3 IL6 CD44-AS1 ARHGDIB TBX15 A2M-AS1 RFTN2 RUBCNL LYL1 LAT2 APELA MEIS3 GALNT15 PTGER3 ST8SIA1 SLC1A6 PRELP MLKL KCNJ2 GFPT2 HLA-F RERG DOCK11 MICU3 PARM1 BMP4 PLSCR4 KLF2 CD44 FRMD6 PGR OSMR ANGPTL2 SHE PCDH12 PKIA GBP4 PPP1R2P4 IL16 RAC2 SEPTIN4 MXRA8 FGD5 NAV3 CTHRC1 IGFBP7 IDO1 RBMS3 PAPPA PLD4 CILP PON3 C4B-AS1 KCND2 ATP8B4 SYNPO WFDC1 ADAMTS10 SNAP25 ADAP2 MME GATM NRP1 SGCD BCHE SERPINB2 TMEM26 C4A-AS1 CD302 ASTN1 CASS4 ELOVL2 DPYSL3 NIBAN1 INMT VAMP5 PTGER2 CORIN ISM1 GUCY1A2 GATA6 ENG ENPP1 GATA4 GDF6 WAS P2RY1 SCG2 LAMA2 HLX TNFRSF8 SERPINA3 RAB31 OLFM4 HOXA-AS2 GEM JPH4 FEZ1 HLA-DOA CR1 DHRS9 SLC2A5 PTPRO PLXNC1 CCN2 SSC5D ODF3B ARHGAP18 OLFML3 APCDD1 SCUBE2 GBP5 PRDM6 EMB HS3ST3B1 SYNPO2 CAMK4 LYPLAL1 STEAP4 PTGDS CALHM5 LIN7A RASGRP3 HS6ST2 CSMD1 RBP7 DLL4 STAB1 SCUBE1 C4A EHD2 ABCA9 GASK1B CSMD2 LCK CD163L1 FGF7 SHOX2 SEMA6B GAL3ST4 LMO2 CADM3-AS1 DLC1 CLMP NFAM1 LAMP5 TSPAN8 NUPR1 KYNU PTPN5 CCN5 FILIP1L CXCL2 MT1M ADAMTS2 SUCNR1 SCN9A TLR1 SERPINF1 PDE2A WIPF1 LAMP5-AS1 SSTR1 CNR1 CADM3 ALOX5 DIO2 ARHGAP31 S100A9 RASSF2 CPED1 DEPP1 ZFP36 CHI3L2 C4B ELFN1 LRRC55 POU2AF1 RGCC COX7A1 PTGIS GPNMB CD248 ST8SIA4 CHRD TMEM158 MMP16 GPC6 GPR78 PSTPIP1 LCP1 NUDT11 CPZ CDC20B CLDN5 TEK GPRIN3 MSRB3 C15orf48 MAGEL2 ZNF521 RGS2 TRPC6 EFEMP1 GLT8D2 MFAP4 BASP1 DUSP1 CD247 KLHDC7B CMKLR1 MFRP C1QTNF5 CTSS HMOX1 IGFBP7-AS1 CCBE1 HS3ST1 MDFIC TMEM119 PEAR1 ANKRD22 TMOD2 G0S2 LILRB3 PELATON CCN2-AS1 PRKCB LINC01018 SLC38A5 LRRC4B TCEAL7 AKT3 GALNT5 ARHGEF15 HECW2 APOL3 FGD2 HMCN1 C1orf162 FERMT3 TFPI CYS1 CLEC4A ARSL JAM3 MARCO ENSG00000233968 HOXD10 GJA1 THBS1 TBX3 BICC1 EDA2R MZB1 AEBP1 S100A8 ENOX1 SLAMF8 RASGRF2 ATP8A2 KCNJ8 FGF1 CASP1 ACAN SLC16A7 PTHLH TRPV2 PROS1 HTRA3 PMP22 C1S PCOLCE AGAP2-AS1 EBI3 PTGS2 CFD TYMP COL6A6 DNM3OS SLC2A3 SPON2 SDS CD79A MEGF10 SAA2 ABCB4 SELPLG SAA2-SAA4 IRAK3 COL16A1 PAPSS2 CXCR6 UBD APOC1 P2RX7 ANPEP RARRES1 IGLV1-51 VIT ECM1 ACVRL1 FLRT2 FMO1 SPATA18 APOBR DACT1 CREB3L1 CCR1 PTPRB TMEM255A PLAGL1 FCGR1A FOS CLMAT3 SPN NEGR1 RGS5 SELL PARVG GJB2 FIBIN CD36 CXCL11 NPL FOSB SAA1 AGAP2 DDR2 CSTA CXCL12 IGLV6-57 HAND2 TNFRSF1B MYO1G COL6A1 FMO2 PODN AMPH AFF3 CNTN3 CALHM6 OLFML2B EBF1 MYO1F SHC2 CYTIP MEDAG MAGI2-AS3 C3orf80 FN1 HLA-DRB6 KLHL6 GNA15 ZEB1 CHIT1 SCIN MMP2 CEACAM7 SULF1 MMP11 CLEC7A IL1B CD68 LAMA4 NLGN4X LRRN3 OLFML1 CXCL8 BCL6B COMP LILRA6 DPYD PTPN7 TRPA1 TNFRSF4 CXCL10 WDFY4 HAS2 NID2 CD8A MAF PWWP3B RUNX1T1 GREM1 CD52 ARHGEF6 ENPP2 CD4 HLA-DRB1 HHIP NCF2 BTK PCOLCE-AS1 GGT5 FBN1 TNFAIP8L2 EGR1 DKK2 KCNMB1 CTSK EDN3 CBLN2 COL21A1 CCL2 PDE4B SPARC NR5A2 VSNL1 NT5E S1PR1 TMEM176A ZBTB16 IFFO1 COLEC12 GNG4 C5AR1 INPP5D VNN1 TNFSF13B MOXD1 C3orf70 IRAG1 MYOCD LDB2 ERG SLC37A2 SLC9A9 MMP1 SMPDL3A GAB3 ESAM GIMAP2 HLA-DRA LRRN4CL CERKL TLR2 STX11 SFMBT2 PIK3CG MAN1A1 CDH5 LPL CDO1 KDR ABCA8 SFRP2 VWF ACTA2 F5 PTPRN2 LHX9 HCLS1 IKZF1 EDNRB XYLT1 IGSF6 AQP9 TSHZ3 TMEM176B OR2I1P IL2RG ADAM23 RHOJ COL8A1 ACTA2-AS1 PID1 CH25H HAVCR2 PIEZO2 FOXF2 EGR2 PRKG1 PIK3R5 ADAMTS12 PLPPR4 CALCRL PDCD1LG2 STAR CSF2RA BGN ADAMTS4 VSTM4 MSC TMEM204 HLA-DQB1 COL6A2 HIC1 COL5A1 NR5A1 APOD ABCA6 CSF3R TLL1 PROX1 LST1 SVEP1 CACNA1H COL5A3 LHFPL6 ABCG2 MSC-AS1 HTRA1 ADGRF5 TIGIT ITGA1 AOAH ZNF469 COL14A1 HLA-DPB1 ANGPT2 NLRP3 DPT HLA-DQB1-AS1 SHISA2 CFH C9 HLA-DPB2 CCND2 DAB2 CST7 SERPINE1 IL21R CMKLR2 TAGAP VGLL3 SRPX2 HBA1 ABI3 PCDH17 PTPN22 RASAL3 TGFBI GNG2 NALF1 MEF2C AOX1 GPR85 PRF1 ITGAM PDLIM3 ADAM12 ITGBL1 HLA-DRB5 EGR3 EDNRA EPYC IL33 HBA2 SIGLEC7 CD34 OSCAR SIGLEC10 ANTXR2 LRRK2 EMILIN1 NR1H4 ITGB2 TREM1 SIGLEC1 DOK2 IL10RA PLCXD3 TLR7 FOLR2 IRF8 HLA-DPA1 JAML TNFAIP6 ABCB1 ARHGAP9 NKG7 COL11A1 HEPH COL5A2 ETV1 COL1A1 CLEC2B TM4SF18 ITGAX PDE10A NDN SPP1 MMP9 THBS2 C1QTNF7 ITM2A INHBA PLN IGHV4-59 ZEB2 PRSS35 DOCK10 CPA3 PLA2G2A HAPLN1 HCK RCSD1 GPR4 TBX18 LPAR6 THBD NNMT A2M MMP13 CCL19 RAMP3 PRRX1 LRRC15 GPM6A IGHV3-74 GMFG SIGLEC9 C11orf96 ITGA4 ISLR LSP1 EDIL3 HLA-DQB2 LINC01094 KLHL4 ECM2 HOPX MGP NID1 HSD11B1 IGHM PRDM1 HK3 CADPS IL2RB SCN7A CDH11 EPHA3 PDGFRB VNN2 FBXL7 COL15A1 ENAM ARHGAP15 ECSCR CCN4 RNASE6 OMD SNX20 SNAI2 PRDM8 PLA2G2D TMIGD3 TFEC APOC4 APOC4-APOC2 KCNE4 ACKR1 RHOH BCL2A1 SELP TLR8 DOCK2 CD14 ITK FLI1 APOC2 LAIR1 COL1A2 RGS4 UBE2QL1 TMEM215 SPARCL1 CD209 TDO2 CXCL14 SPI1 VCAN TPSB2 TPSAB1 FABP4 EPB41L3 BIN2 TMEM200A ITGAL TWIST1 ITGA8 SRGN FNDC1 MEG3 NDNF ITGA11 NTM PDGFRA CNTN1 DOK6 GIMAP1 VCAN-AS1 CCR2 CCL21 DLK1 NCF4 LY86 FLT1 MPEG1 ASPN OGN CSF2RB FYB1 VAT1L CYBB TNFSF8 EMCN CYTH4 ROBO4 FGR C1QTNF1 P2RY8 GIMAP8 IGHV3-48 ADH1B CLEC4E GIMAP5 PCED1B-AS1 GPR84 FGL2 VCAM1 IGHV1-24 CD300A SLA CLEC14A CD3E APBB1IP CDH13 CXCL13 COL10A1 CD300E HLA-DQA2 CD28 FAP SIRPB2 LINC01929 CCL11 ARX SASH3 CD86 HGF CD180 IGHV4-31 CCL8 NRK DIPK2B APLNR LY96 SAMSN1 LILRB1 ADGRL4 LYZ SFRP4 TRBC2 CSF1R CNRIP1 OLR1 MMRN1 LRRC25 MYCT1 LINC01614 F13A1 LUM POSTN FOXF1 EVI2B ALOX5AP CD53 IL2RA GPR183 GPR34 COL6A3 NCKAP1L HLA-DQA1 GYPC LAPTM5 JCHAIN FCER1G IGKV1-17 PTPRC IL7R SLAMF7 AIF1 OSM PLEK EVI2A FCGR2A FCGR2C IGHV1-46 SLCO2B1 GIMAP6 IGHV4-39 CD48 TLR4 C3AR1 ESM1 TCF21 CLEC5A MSR1 IGHV1-69 LILRB2 COL3A1 MS4A4A GIMAP4 IGHV2-26 CD163 GZMA GIMAP7 GZMK TREM2 IGHV3-66 LCP2 MNDA ADAMDEC1 HBB MS4A7 CD84 FPR3 IGKV3-15 IGHV1-3 CD1E LYVE1 FPR1 IGHV2-5 IGHV3-15 IGLV1-44 IGKV4-1 IGHV3-33 IGHJ6 CCR5 CD2 FCGR3A IGHG1 IGHA2 IGHV3-21 IGLJ2 MS4A6A IGHA1 IGHV1-2 TYROBP IGHV3-7 CXCL9 IGKV1-16 CD93 CLEC10A IGKV3D-15 IGHV5-51 LILRB4 IGHV3-53 DCN IGLC3 IGLC2 IGLV3-10 IGKJ2 C7 IGKV3D-11 C1QB C1QA IGLV3-19 GPR65 IGKJ5 IGKC IGLV1-47 IGKJ3 C1QC IGKV3-11 FCGR3B IGHV3-11 RGS1 IGHG3 IGHV1-18 FCN1 FCGR2B IGLV1-40 IGHG2 IGKV3D-20 IGHG4 IGLV5-45 IGKV3-20 COPDA1 IGLJ1 HOXC12 IGKJ1 IGLV2-11 IGKV1-12 IGLV2-23 IGLL5 IGLV3-25 IGLC1 VSIG4 IGKJ4 IGLV3-1 IGHGP IGKV1-5 IGLV3-21 IGKV1-9 IGLV2-14 IGHV3-23
BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_UP http://www.gsea-msigdb.org/gsea/msigdb/human/geneset/BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_UP CCN1 VCAN COL12A1 THBS1 ITGAV TFPI2 APP ANKRD1 GPC4 SEMA3C GANAB EGR1 ATP6AP2 ITGB4 ADAM9 GBA NUP210 DSG2 OS9 COL4A2
There are three columns, the pathway, the source and the genes in the pathway
I have read this into R using read.delim but the 3rd column onwards is read in as multiple tab separated columns dependant on the number of genes in that pathway (there are 6000 pathways in total).
I would like to concatenate all columns from the third column onwards to that they are comma seperated. So the first line as an example output would be:
SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM http://www.gsea-msigdb.org/gsea/msigdb/human/geneset/SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM ADGRV1,MAP3K7CL,CLEC3B,SLC1A3,STN1
I know how to use paste0 but I am unsure how to do it when each row has a different number of columns beyond the third column.
Any help would be much appreciated.
Many thanks
CodePudding user response：
you can simply use unite and the column indexes. See example:
library(tidyverse)
mtcars |>
unite(val, 4:ncol(mtcars), sep = ",")
#> mpg cyl disp val
#> Mazda RX4 21.0 6 160.0 110,3.9,2.62,16.46,0,1,4,4
#> Mazda RX4 Wag 21.0 6 160.0 110,3.9,2.875,17.02,0,1,4,4
#> Datsun 710 22.8 4 108.0 93,3.85,2.32,18.61,1,1,4,1
#> Hornet 4 Drive 21.4 6 258.0 110,3.08,3.215,19.44,1,0,3,1
#> Hornet Sportabout 18.7 8 360.0 175,3.15,3.44,17.02,0,0,3,2
#> Valiant 18.1 6 225.0 105,2.76,3.46,20.22,1,0,3,1
#> Duster 360 14.3 8 360.0 245,3.21,3.57,15.84,0,0,3,4
#> Merc 240D 24.4 4 146.7 62,3.69,3.19,20,1,0,4,2
#> Merc 230 22.8 4 140.8 95,3.92,3.15,22.9,1,0,4,2
#> Merc 280 19.2 6 167.6 123,3.92,3.44,18.3,1,0,4,4
#> Merc 280C 17.8 6 167.6 123,3.92,3.44,18.9,1,0,4,4
#> Merc 450SE 16.4 8 275.8 180,3.07,4.07,17.4,0,0,3,3
#> Merc 450SL 17.3 8 275.8 180,3.07,3.73,17.6,0,0,3,3
#> Merc 450SLC 15.2 8 275.8 180,3.07,3.78,18,0,0,3,3
#> Cadillac Fleetwood 10.4 8 472.0 205,2.93,5.25,17.98,0,0,3,4
#> Lincoln Continental 10.4 8 460.0 215,3,5.424,17.82,0,0,3,4
#> Chrysler Imperial 14.7 8 440.0 230,3.23,5.345,17.42,0,0,3,4
#> Fiat 128 32.4 4 78.7 66,4.08,2.2,19.47,1,1,4,1
#> Honda Civic 30.4 4 75.7 52,4.93,1.615,18.52,1,1,4,2
#> Toyota Corolla 33.9 4 71.1 65,4.22,1.835,19.9,1,1,4,1
#> Toyota Corona 21.5 4 120.1 97,3.7,2.465,20.01,1,0,3,1
#> Dodge Challenger 15.5 8 318.0 150,2.76,3.52,16.87,0,0,3,2
#> AMC Javelin 15.2 8 304.0 150,3.15,3.435,17.3,0,0,3,2
#> Camaro Z28 13.3 8 350.0 245,3.73,3.84,15.41,0,0,3,4
#> Pontiac Firebird 19.2 8 400.0 175,3.08,3.845,17.05,0,0,3,2
#> Fiat X1-9 27.3 4 79.0 66,4.08,1.935,18.9,1,1,4,1
#> Porsche 914-2 26.0 4 120.3 91,4.43,2.14,16.7,0,1,5,2
#> Lotus Europa 30.4 4 95.1 113,3.77,1.513,16.9,1,1,5,2
#> Ford Pantera L 15.8 8 351.0 264,4.22,3.17,14.5,0,1,5,4
#> Ferrari Dino 19.7 6 145.0 175,3.62,2.77,15.5,0,1,5,6
#> Maserati Bora 15.0 8 301.0 335,3.54,3.57,14.6,0,1,5,8
#> Volvo 142E 21.4 4 121.0 109,4.11,2.78,18.6,1,1,4,2