read_geneset.RdFunction to read various geneset file formats and returns a list of vectors containing gene names.
read_geneset(x, min_size = 15)
| x | file, |
|---|---|
| min_size | minimum size of geneset otherwise filter out. |
Returns a list of gene sets
gmt_file <- system.file("extdata", "h.all.v7.4.symbols.gmt", package = "bowerbird") gs <- read_geneset(gmt_file) head(gs) #> $HALLMARK_TNFA_SIGNALING_VIA_NFKB #> [1] "JUNB" "CXCL2" "ATF3" "NFKBIA" "TNFAIP3" "PTGS2" #> [7] "CXCL1" "IER3" "CD83" "CCL20" "CXCL3" "MAFF" #> [13] "NFKB2" "TNFAIP2" "HBEGF" "KLF6" "BIRC3" "PLAUR" #> [19] "ZFP36" "ICAM1" "JUN" "EGR3" "IL1B" "BCL2A1" #> [25] "PPP1R15A" "ZC3H12A" "SOD2" "NR4A2" "IL1A" "RELB" #> [31] "TRAF1" "BTG2" "DUSP1" "MAP3K8" "ETS2" "F3" #> [37] "SDC4" "EGR1" "IL6" "TNF" "KDM6B" "NFKB1" #> [43] "LIF" "PTX3" "FOSL1" "NR4A1" "JAG1" "CCL4" #> [49] "GCH1" "CCL2" "RCAN1" "DUSP2" "EHD1" "IER2" #> [55] "REL" "CFLAR" "RIPK2" "NFKBIE" "NR4A3" "PHLDA1" #> [61] "IER5" "TNFSF9" "GEM" "GADD45A" "CXCL10" "PLK2" #> [67] "BHLHE40" "EGR2" "SOCS3" "SLC2A6" "PTGER4" "DUSP5" #> [73] "SERPINB2" "NFIL3" "SERPINE1" "TRIB1" "TIPARP" "RELA" #> [79] "BIRC2" "CXCL6" "LITAF" "TNFAIP6" "CD44" "INHBA" #> [85] "PLAU" "MYC" "TNFRSF9" "SGK1" "TNIP1" "NAMPT" #> [91] "FOSL2" "PNRC1" "ID2" "CD69" "IL7R" "EFNA1" #> [97] "PHLDA2" "PFKFB3" "CCL5" "YRDC" "IFNGR2" "SQSTM1" #> [103] "BTG3" "GADD45B" "KYNU" "G0S2" "BTG1" "MCL1" #> [109] "VEGFA" "MAP2K3" "CDKN1A" "CCN1" "TANK" "IFIT2" #> [115] "IL18" "TUBB2A" "IRF1" "FOS" "OLR1" "RHOB" #> [121] "AREG" "NINJ1" "ZBTB10" "PLPP3" "KLF4" "CXCL11" #> [127] "SAT1" "CSF1" "GPR183" "PMEPA1" "PTPRE" "TLR2" #> [133] "ACKR3" "KLF10" "MARCKS" "LAMB3" "CEBPB" "TRIP10" #> [139] "F2RL1" "KLF9" "LDLR" "TGIF1" "RNF19B" "DRAM1" #> [145] "B4GALT1" "DNAJB4" "CSF2" "PDE4B" "SNN" "PLEK" #> [151] "STAT5A" "DENND5A" "CCND1" "DDX58" "SPHK1" "CD80" #> [157] "TNFAIP8" "CCNL1" "FUT4" "CCRL2" "SPSB1" "TSC22D1" #> [163] "B4GALT5" "SIK1" "CLCF1" "NFE2L2" "FOSB" "PER1" #> [169] "NFAT5" "ATP2B1" "IL12B" "IL6ST" "SLC16A6" "ABCA1" #> [175] "HES1" "BCL6" "IRS2" "SLC2A3" "CEBPD" "IL23A" #> [181] "SMAD3" "TAP1" "MSC" "IFIH1" "IL15RA" "TNIP2" #> [187] "BCL3" "PANX1" "FJX1" "EDN1" "EIF1" "BMP2" #> [193] "DUSP4" "PDLIM5" "ICOSLG" "GFPT2" "KLF2" "TNC" #> [199] "SERPINB8" "MXD1" #> #> $HALLMARK_HYPOXIA #> [1] "PGK1" "PDK1" "GBE1" "PFKL" "ALDOA" "ENO2" #> [7] "PGM1" "NDRG1" "HK2" "ALDOC" "GPI" "MXI1" #> [13] "SLC2A1" "P4HA1" "ADM" "P4HA2" "ENO1" "PFKP" #> [19] "AK4" "FAM162A" "PFKFB3" "VEGFA" "BNIP3L" "TPI1" #> [25] "ERO1A" "KDM3A" "CCNG2" "LDHA" "GYS1" "GAPDH" #> [31] "BHLHE40" "ANGPTL4" "JUN" "SERPINE1" "LOX" "GCK" #> [37] "PPFIA4" "MAFF" "DDIT4" "SLC2A3" "IGFBP3" "NFIL3" #> [43] "FOS" "RBPJ" "HK1" "CITED2" "ISG20" "GALK1" #> [49] "WSB1" "PYGM" "STC1" "ZNF292" "BTG1" "PLIN2" #> [55] "CSRP2" "VLDLR" "JMJD6" "EXT1" "F3" "PDK3" #> [61] "ANKZF1" "UGP2" "ALDOB" "STC2" "ERRFI1" "ENO3" #> [67] "PNRC1" "HMOX1" "PGF" "GAPDHS" "CHST2" "TMEM45A" #> [73] "BCAN" "ATF3" "CAV1" "AMPD3" "GPC3" "NDST1" #> [79] "IRS2" "SAP30" "GAA" "SDC4" "STBD1" "IER3" #> [85] "PKLR" "IGFBP1" "PLAUR" "CAVIN3" "CCN5" "LARGE1" #> [91] "NOCT" "S100A4" "RRAGD" "ZFP36" "EGFR" "EDN2" #> [97] "IDS" "CDKN1A" "RORA" "DUSP1" "MIF" "PPP1R3C" #> [103] "DPYSL4" "KDELR3" "DTNA" "ADORA2B" "HS3ST1" "CAVIN1" #> [109] "NR3C1" "KLF6" "GPC4" "CCN1" "TNFAIP3" "CA12" #> [115] "HEXA" "BGN" "PPP1R15A" "PGM2" "PIM1" "PRDX5" #> [121] "NAGK" "CDKN1B" "BRS3" "TKTL1" "MT1E" "ATP7A" #> [127] "MT2A" "SDC3" "TIPARP" "PKP1" "ANXA2" "PGAM2" #> [133] "DDIT3" "PRKCA" "SLC37A4" "CXCR4" "EFNA3" "CP" #> [139] "KLF7" "CCN2" "CHST3" "TPD52" "LXN" "B4GALNT2" #> [145] "PPARGC1A" "BCL2" "GCNT2" "HAS1" "KLHL24" "SCARB1" #> [151] "SLC25A1" "SDC2" "CASP6" "VHL" "FOXO3" "PDGFB" #> [157] "B3GALT6" "SLC2A5" "SRPX" "EFNA1" "GLRX" "ACKR3" #> [163] "PAM" "TGFBI" "DCN" "SIAH2" "PLAC8" "FBP1" #> [169] "TPST2" "PHKG1" "MYH9" "CDKN1C" "GRHPR" "PCK1" #> [175] "INHA" "HSPA5" "NDST2" "NEDD4L" "TPBG" "XPNPEP1" #> [181] "IL6" "SLC6A6" "MAP3K1" "LDHC" "AKAP12" "TES" #> [187] "KIF5A" "LALBA" "COL5A1" "GPC1" "HDLBP" "ILVBL" #> [193] "NCAN" "TGM2" "ETS1" "HOXB9" "SELENBP1" "FOSL2" #> [199] "SULT2B1" "TGFB3" #> #> $HALLMARK_CHOLESTEROL_HOMEOSTASIS #> [1] "FDPS" "CYP51A1" "IDI1" "FDFT1" "DHCR7" "SQLE" #> [7] "HMGCS1" "NSDHL" "LSS" "MVD" "LDLR" "TM7SF2" #> [13] "ALDOC" "EBP" "SCD" "PMVK" "MVK" "LPL" #> [19] "SC5D" "FADS2" "HMGCR" "HSD17B7" "ANXA13" "SREBF2" #> [25] "PCYT2" "ACSS2" "ATF3" "ADH4" "ETHE1" "ECH1" #> [31] "CBS" "GUSB" "FASN" "LGALS3" "ATF5" "ANXA5" #> [37] "TP53INP1" "CHKA" "GSTM2" "ACAT2" "AVPR1A" "PLSCR1" #> [43] "CLU" "ERRFI1" "TRIB3" "CXCL16" "TNFRSF12A" "ACTG1" #> [49] "JAG1" "LGMN" "FBXO6" "GPX8" "PNRC1" "ANTXR2" #> [55] "MAL2" "CD9" "PPARG" "GLDC" "STX5" "STARD4" #> [61] "CTNNB1" "TMEM97" "NIBAN1" "PDK3" "PLAUR" "SEMA3B" #> [67] "GNAI1" "ABCA2" "ATXN2" "NFIL3" "ALCAM" "FABP5" #> [73] "S100A11" "CPEB2" #> #> $HALLMARK_MITOTIC_SPINDLE #> [1] "ARHGEF2" "CLASP1" "KIF11" "KIF23" "ALS2" "ARF6" #> [7] "MYO9B" "MYH9" "TUBGCP3" "CKAP5" "RACGAP1" "PREX1" #> [13] "ARHGEF3" "NUMA1" "SPTBN1" "KIF2C" "KIF5B" "TTK" #> [19] "APC" "CEP250" "PAFAH1B1" "CDC42EP2" "KIF3B" "CCDC88A" #> [25] "KIF15" "BIRC5" "CNTROB" "NF1" "TSC1" "CDC27" #> [31] "CNTRL" "TUBGCP5" "KIF4A" "MAPRE1" "FGD6" "BRCA2" #> [37] "PLK1" "RASA1" "NEK2" "WASF1" "TOP2A" "TRIO" #> [43] "ARHGEF11" "KATNB1" "PRC1" "ANLN" "CDK5RAP2" "SMC3" #> [49] "TUBGCP2" "ESPL1" "MAP1S" "ARHGAP27" "DOCK4" "SAC3D1" #> [55] "INCENP" "ARHGAP5" "GSN" "NET1" "LRPPRC" "RABGAP1" #> [61] "FLNB" "ARAP3" "FGD4" "ABR" "CENPJ" "NCK1" #> [67] "CENPF" "KIF20B" "WASF2" "MYH10" "CENPE" "CYTH2" #> [73] "MID1" "KLC1" "MARK4" "ARL8A" "CEP57" "UXT" #> [79] "ARHGAP4" "CDC42EP4" "SASS6" "LATS1" "OPHN1" "WASL" #> [85] "MAP3K11" "SOS1" "ABL1" "TIAM1" "KIF1B" "ITSN1" #> [91] "SHROOM1" "NCK2" "DLGAP5" "BCR" "RANBP9" "EPB41L2" #> [97] "SEPTIN9" "KATNA1" "TUBD1" "TPX2" "KIF3C" "SHROOM2" #> [103] "TUBGCP6" "SPTAN1" "PALLD" "ARFIP2" "KNTC1" "HOOK3" #> [109] "SUN2" "MID1IP1" "DLG1" "FLNA" "ARHGAP10" "CDC42BPA" #> [115] "ARHGEF12" "MARCKS" "NIN" "PCM1" "RALBP1" "EZR" #> [121] "SSH2" "CDK1" "RAB3GAP1" "FARP1" "SYNPO" "RHOF" #> [127] "ECT2" "EPB41" "RAPGEF6" "KIF22" "PCGF5" "STAU1" #> [133] "ARHGDIA" "AURKA" "FBXO5" "NUSAP1" "PXN" "BCAR1" #> [139] "CD2AP" "AKAP13" "HDAC6" "CEP131" "LLGL1" "ATG4B" #> [145] "PCNT" "ALMS1" "KPTN" "DST" "KIFAP3" "PPP4R2" #> [151] "ARHGAP29" "RASAL2" "CCNB2" "PIF1" "RASA2" "NEDD9" #> [157] "SMC1A" "ACTN4" "PKD2" "CLIP2" "CDC42" "NDC80" #> [163] "TLK1" "TAOK2" "TBCD" "CAPZB" "DOCK2" "CTTN" #> [169] "SMC4" "ARFGEF1" "TUBA4A" "LMNB1" "ABI1" "ROCK1" #> [175] "CEP192" "BUB1" "GEMIN4" "PLEKHG2" "RICTOR" "BCL2L11" #> [181] "DYNC1H1" "FSCN1" "ARHGEF7" "DYNLL2" "MYO1E" "BIN1" #> [187] "NOTCH2" "RFC1" "PDLIM5" "RHOT2" "SORBS2" "CDC42EP1" #> [193] "VCL" "CLIP1" "STK38L" "YWHAE" "RAPGEF5" "CEP72" #> [199] "CSNK1D" #> #> $HALLMARK_WNT_BETA_CATENIN_SIGNALING #> [1] "MYC" "CTNNB1" "JAG2" "NOTCH1" "DLL1" "AXIN2" "PSEN2" "FZD1" #> [9] "NOTCH4" "LEF1" "AXIN1" "NKD1" "WNT5B" "CUL1" "JAG1" "MAML1" #> [17] "KAT2A" "GNAI1" "WNT6" "PTCH1" "NCOR2" "DKK4" "HDAC2" "DKK1" #> [25] "TCF7" "WNT1" "NUMB" "ADAM17" "DVL2" "PPARD" "NCSTN" "HDAC5" #> [33] "CCND2" "FRAT1" "CSNK1E" "RBPJ" "FZD8" "TP53" "SKP2" "HEY2" #> [41] "HEY1" "HDAC11" #> #> $HALLMARK_TGF_BETA_SIGNALING #> [1] "TGFBR1" "SMAD7" "TGFB1" "SMURF2" "SMURF1" "BMPR2" #> [7] "SKIL" "SKI" "ACVR1" "PMEPA1" "NCOR2" "SERPINE1" #> [13] "JUNB" "SMAD1" "SMAD6" "PPP1R15A" "TGIF1" "FURIN" #> [19] "SMAD3" "FKBP1A" "MAP3K7" "BMPR1A" "CTNNB1" "HIPK2" #> [25] "KLF10" "BMP2" "ENG" "APC" "PPM1A" "XIAP" #> [31] "CDH1" "ID1" "LEFTY2" "CDKN1C" "TRIM33" "RAB31" #> [37] "TJP1" "SLC20A1" "CDK9" "ID3" "NOG" "ARID4B" #> [43] "IFNGR2" "ID2" "PPP1CA" "SPTBN1" "WWTR1" "BCAR3" #> [49] "THBS1" "FNTA" "HDAC1" "UBE2D3" "LTBP2" "RHOA" #>