addTFBS() breaks for mm10 on HOCOMOCO
When I run:
> GRN = addTFBS(GRN, motifFolder = motifFolder, TFs = "all", filesTFBSPattern = "_TFBS",
+ fileEnding = ".bed.gz", forceRerun = TRUE)
Following the standard tutorial but with mm10 data and the HOCOMOCO mm10 database provided by you I get the following error:
INFO [2023-05-15 11:30:49] Checking database folder for matching files: /PWMScan_HOCOMOCOv10
INFO [2023-05-15 11:30:49] Found 422 matching TFs: AHR, AIRE, ALX1, ANDR, AP2A, AP2B, AP2C, AP2D, ARI3A.D, ARI3A.S, ARI5B, ARNT, ARNT2, ATF1, ATF2, ATF3, ATOH1, BACH1, BARX2, BATF, BCL6, BHE40, BMAL1, BRAC, BRCA1, CDC5L, CDX1, CDX2, CEBPA, CEBPB, CEBPD, CEBPE, CEBPG, CEBPZ, COE1, COT1.B, COT1.S, COT2.B, COT2.S, CREB1, CREM, CRX.A, CRX.S, CTCF, CUX1, CXXC1, DBP, DDIT3, DLX2, DLX3, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, E2F7, E4F1, EGR1, EGR2, EGR3, EGR4, EHF, ELF1, ELF2, ELF3, ELF5, ELK1, ELK3, ELK4, ENOA, EPAS1, ERG, ERR1, ERR2, ERR3, ESR1, ESR2.B, ESR2.S, ETS1, ETS2, ETV4, ETV5, EVI1, EVX1, EVX2, FEV, FLI1, FOS, FOSB, FOSL1, FOSL2, FOXA1, FOXA2, FOXA3, FOXC1, FOXC2, FOXD1, FOXD3, FOXF1, FOXF2, FOXI1, FOXJ2, FOXJ3.A, FOXJ3.S, FOXM1, FOXO1, FOXO3, FOXO4, FOXP2, FOXP3, FOXQ1, FUBP1, GABP1, GABPA, GATA1, GATA2, GATA3, GATA4, GATA5, GATA6, GCM1, GCR.C, GCR.S, GFI1, GFI1B, GLI1, GLI2, GLI3, GLIS3, HAND1, HBP1, HEN1, HES1, HESX1, HEY2, HIC1, HIF1A, HINFP, HLF, HLTF, HMGA1, HMGA2, HNF1A, HNF1B, HNF4A, HNF4G, HNF6, HSF1, HSF2, HTF4, HXA1, HXA10, HXA13, HXA5, HXA7, HXA9, HXB1, HXB6, HXB7, HXB8, HXC6, HXC8, HXD10, HXD13, HXD4, HXD9, IKZF1, INSM1, IRF1, IRF2, IRF3, IRF4, IRF5, IRF7, IRF8, IRF9, ISL1, ITF2, JUN, JUNB, JUND, KAISO, KLF1, KLF15, KLF3, KLF4, KLF6, KLF8, LEF1, LHX2, LHX3, MAF, MAFA, MAFB, MAFG, MAFK.A, MAFK.S, MAX, MAZ, MBD2, MCR, MECP2, MEF2A, MEF2C, MEF2D, MEIS1, MEIS2, MITF, MLXPL, MSX2, MSX3, MTF1, MXI1, MYB, MYBB, MYC, MYCN, MYF6, MYOD1, MYOG, NANOG.A, NANOG.S, NDF1, NF2L1, NF2L2, NFAC1.A, NFAC1.S, NFAC2, NFAC3, NFAC4, NFAT5, NFE2, NFIA.C, NFIA.S, NFIL3, NFKB1, NFKB2, NFYA.D, NFYA.S, NFYB, NFYC, NKX21, NKX22, NKX25, NKX28, NKX31, NKX32, NOBOX, NR0B1, NR1D1, NR1H2, NR1H4, NR1I2.S, NR1I3.S, NR2C1, NR2C2, NR2E3, NR2F6, NR4A1, NR4A2, NR4A3, NR5A2, NR6A1, NRF1, OLIG2, ONEC2, OTX1, OTX2, OVOL1, P53, P63, P73, PAX2.D, PAX2.S, PAX5.D, PAX5.S, PAX6, PAX8, PBX1, PBX2, PBX3, PDX1, PEBB, PIT1, PITX2, PKNX1, PLAG1.D, PLAG1.S, PO2F1, PO2F2, PO3F1, PO3F2, PO4F2, PO5F1, PO6F1, PPARA.C, PPARA.S, PPARD, PPARG.A, PPARG.S, PRD14, PRDM1, PRGR.C, PRGR.S, PROP1, PRRX1, PRRX2, PTF1A, PURA, RARA.C, RARA.S, RARB, RARG.C, RARG.S, REL, RELB, REST, RFX1, RFX2, RFX3, RORA, RORG, RREB1, RUNX1, RUNX2, RUNX3, RXRA, RXRB, RXRG, SMAD1, SMAD2, SMAD3, SMAD4, SMRC1, SNAI1, SNAI2, SOX10, SOX13, SOX15, SOX17, SOX18, SOX2, SOX3, SOX4, SOX5, SOX9, SP1.A, SP1.S, SP2, SP3, SP4, SPI1, SPIB, SPZ1, SRBP1, SRBP2, SRF, SRY, STA5A, STA5B, STAT1, STAT2, STAT3, STAT4, STAT6, STF1, SUH, TAL1.A, TAL1.S, TBP, TBX2, TBX20, TBX3, TBX5, TCF7, TEAD1, TEAD3, TEAD4, TEF, TF2L1, TF65.C, TF65.S, TF7L2, TFCP2, TFDP1, TFE2.A, TFE2.S, TFE3, TFEB, TGIF1.S, THA.C, THA.S, THB.C, THB.S, TLX1.D, TLX1.S, TWST1, TYY1, UBIP1, USF1, USF2, VDR.C, VDR.S, VSX2, WT1, XBP1, YBOX1, ZBT18, ZBT7A, ZBTB6, ZEB1, ZEP1, ZEP2, ZFHX3, ZFX, ZIC1, ZIC2, ZIC3, ZN143, ZN148, ZN423
INFO [2023-05-15 11:30:49] Use all TF from the database folder /PWMScan_HOCOMOCOv10
INFO [2023-05-15 11:30:49] Reading file /PWMScan_HOCOMOCOv10/translationTable.csv
INFO [2023-05-15 11:30:49] Finished successfully. Execution time: 0 secs
INFO [2023-05-15 11:30:49] Filtering the following 422 TFs as they are not present in the RNA-Seq data: AHR,AIRE,ALX1,ANDR,AP2A,AP2B,AP2C,AP2D,ARI3A.D,ARI3A.S,ARI5B,ARNT,ARNT2,ATF1,ATF2,ATF3,ATOH1,BACH1,BARX2,BATF,BCL6,BHE40,BMAL1,BRAC,BRCA1,CDC5L,CDX1,CDX2,CEBPA,CEBPB,CEBPD,CEBPE,CEBPG,CEBPZ,COE1,COT1.B,COT1.S,COT2.B,COT2.S,CREB1,CREM,CRX.A,CRX.S,CTCF,CUX1,CXXC1,DBP,DDIT3,DLX2,DLX3,E2F1,E2F2,E2F3,E2F4,E2F5,E2F6,E2F7,E4F1,EGR1,EGR2,EGR3,EGR4,EHF,ELF1,ELF2,ELF3,ELF5,ELK1,ELK3,ELK4,ENOA,EPAS1,ERG,ERR1,ERR2,ERR3,ESR1,ESR2.B,ESR2.S,ETS1,ETS2,ETV4,ETV5,EVI1,EVX1,EVX2,FEV,FLI1,FOS,FOSB,FOSL1,FOSL2,FOXA1,FOXA2,FOXA3,FOXC1,FOXC2,FOXD1,FOXD3,FOXF1,FOXF2,FOXI1,FOXJ2,FOXJ3.A,FOXJ3.S,FOXM1,FOXO1,FOXO3,FOXO4,FOXP2,FOXP3,FOXQ1,FUBP1,GABP1,GABPA,GATA1,GATA2,GATA3,GATA4,GATA5,GATA6,GCM1,GCR.C,GCR.S,GFI1,GFI1B,GLI1,GLI2,GLI3,GLIS3,HAND1,HBP1,HEN1,HES1,HESX1,HEY2,HIC1,HIF1A,HINFP,HLF,HLTF,HMGA1,HMGA2,HNF1A,HNF1B,HNF4A,HNF4G,HNF6,HSF1,HSF2,HTF4,HXA1,HXA10,HXA13,HXA5,HXA7,HXA9,HXB1,HXB6,HXB7,HXB8,HXC6,HXC8,HXD10,HXD13,HXD4,HXD9,IKZF1,INSM1,IRF1,IRF2,IRF3,IRF4,IRF5,IRF7,IRF8,IRF9,ISL1,ITF2,JUN,JUNB,JUND,KAISO,KLF1,KLF15,KLF3,KLF4,KLF6,KLF8,LEF1,LHX2,LHX3,MAF,MAFA,MAFB,MAFG,MAFK.A,MAFK.S,MAX,MAZ,MBD2,MCR,MECP2,MEF2A,MEF2C,MEF2D,MEIS1,MEIS2,MITF,MLXPL,MSX2,MSX3,MTF1,MXI1,MYB,MYBB,MYC,MYCN,MYF6,MYOD1,MYOG,NANOG.A,NANOG.S,NDF1,NF2L1,NF2L2,NFAC1.A,NFAC1.S,NFAC2,NFAC3,NFAC4,NFAT5,NFE2,NFIA.C,NFIA.S,NFIL3,NFKB1,NFKB2,NFYA.D,NFYA.S,NFYB,NFYC,NKX21,NKX22,NKX25,NKX28,NKX31,NKX32,NOBOX,NR0B1,NR1D1,NR1H2,NR1H4,NR1I2.S,NR1I3.S,NR2C1,NR2C2,NR2E3,NR2F6,NR4A1,NR4A2,NR4A3,NR5A2,NR6A1,NRF1,OLIG2,ONEC2,OTX1,OTX2,OVOL1,P53,P63,P73,PAX2.D,PAX2.S,PAX5.D,PAX5.S,PAX6,PAX8,PBX1,PBX2,PBX3,PDX1,PEBB,PIT1,PITX2,PKNX1,PLAG1.D,PLAG1.S,PO2F1,PO2F2,PO3F1,PO3F2,PO4F2,PO5F1,PO6F1,PPARA.C,PPARA.S,PPARD,PPARG.A,PPARG.S,PRD14,PRDM1,PRGR.C,PRGR.S,PROP1,PRRX1,PRRX2,PTF1A,PURA,RARA.C,RARA.S,RARB,RARG.C,RARG.S,REL,RELB,REST,RFX1,RFX2,RFX3,RORA,RORG,RREB1,RUNX1,RUNX2,RUNX3,RXRA,RXRB,RXRG,SMAD1,SMAD2,SMAD3,SMAD4,SMRC1,SNAI1,SNAI2,SOX10,SOX13,SOX15,SOX17,SOX18,SOX2,SOX3,SOX4,SOX5,SOX9,SP1.A,SP1.S,SP2,SP3,SP4,SPI1,SPIB,SPZ1,SRBP1,SRBP2,SRF,SRY,STA5A,STA5B,STAT1,STAT2,STAT3,STAT4,STAT6,STF1,SUH,TAL1.A,TAL1.S,TBP,TBX2,TBX20,TBX3,TBX5,TCF7,TEAD1,TEAD3,TEAD4,TEF,TF2L1,TF65.C,TF65.S,TF7L2,TFCP2,TFDP1,TFE2.A,TFE2.S,TFE3,TFEB,TGIF1.S,THA.C,THA.S,THB.C,THB.S,TLX1.D,TLX1.S,TWST1,TYY1,UBIP1,USF1,USF2,VDR.C,VDR.S,VSX2,WT1,XBP1,YBOX1,ZBT18,ZBT7A,ZBTB6,ZEB1,ZEP1,ZEP2,ZFHX3,ZFX,ZIC1,ZIC2,ZIC3,ZN143,ZN148,ZN423
ERROR [2023-05-15 11:30:49] No shared Tfs.
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# An error occurred. See details above. If you think this is a bug, please contact us. #
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Error in .checkAndLogWarningsAndErrors(NULL, message, isWarning = FALSE) :
No shared Tfs.
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# An error occurred. See details above. If you think this is a bug, please contact us. #
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Any clue why this is happening?
Thank you