GeorgescuC
commented
1 year ago Hi @sheilak97 ,
Looking at the log, it appears the issue happens when trying to run a PCA (which we now do as default preprocessing before running the Leiden algorithm when building the neighbors graph). Since the "unassigned" annotation has less than 20 cells (default k_nn) it should not try to run the PCA on it at all and simply return one cluster for that annotation, but no other log message indicates it has moved on to another annotation or the per chromosome subclustering.
Could you check that you are running the latest version of infercnv (1.14.0)? If you are, would you be able to privately share the backup object from the last step that successfully completed so I can look into the issue?
Regards, Christophe.
Hello, I recently updated my R studio to the latest version, and I tried to re-run to the infercnv codes I previously ran successfully, and got the following error warning after "Centering and scaling data matrix" in step 15:
Error in irlba(A = t(x = object), nv = npcs, ...) : max(nu, nv) must be strictly less than min(nrow(A), ncol(A))
Also when I tried to remove infercnv and reinstall I couldn't find it using remove.packages. Any idea how I can fix this? Thanks.
My command used: infercnv_obj6 = infercnv::run(infercnv_obj6, cutoff=0.1, out_dir=paste0("/Users/sheilak/Desktop/CNV_lib2_noChrXY"), cluster_by_groups = T, cluster_references = F, final_center_val = 1, denoise = T, HMM = T, num_threads=4, output_format = "png", useRaster = T)
Below is the printing of my console:
INFO [2022-12-09 16:50:24] define_signif_tumor_subclusters(p_val=0.1 INFO [2022-12-09 16:50:24] define_signif_tumorsubclusters(), tumor: 0 Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |=====================================================================================| 100% PC 1 Positive: SP3, OLA1, ITGA6, CIR1, HAT1, MTX2, HNRNPA3, DYNC1I2, NFE2L2, DCAF17 AGPS, METTL8, SESTD1, TLK1, CWC22, GORASP2, UBE2E3, DNAJC10, NCKAP1, UBR3 NUP35, ZC3H15, METTL5, AC007319.1, SSB, TFPI, GULP1, KLHL23, PPIG, WDR75 Negative: MBD3, UQCR11, MEX3D, TCF3, ABHD17A, RPS15, CSNK1G2, MKNK2, AP3D1, PLEKHJ1 OAZ1, DAZAP1, LSM7, NDUFS7, TIMM13, CIRBP, LMNB2, MIDN, GADD45B, GPX4 SLC39A3, POLR2E, CNN2, SGTA, TMEM259, THOP1, WDR18, ARID3A, NCLN, PTBP1 PC 2 Positive: WEE1, ZNF143, SWAP70, IPO7, SBF2, TMEM41B, PARVA, MICAL2, USP47, EIF4G2 DENND5A, CTR9, TEAD1, MTRNR2L8, TMEM9B, AMPD3, ADM, RPL27A, LINC00958, EIF3F BTBD10, PPFIBP2, FAR1, MRPL17, RRAS2, TAF10, COPB1, ILK, PSMA1, TIMM10B Negative: MALAT1, NEAT1, RNASEH2C, OVOL1, FIBP, CFL1, CCDC85B, DRAP1, SART1, DPF2 EIF1AD, BANF1, SF3B2, CAPN1, PACS1, RAB1B, S100A14, S100A13, YIF1A, MRPL49 CHTOP, S100A16, BRMS1, ILF2, GATAD2B, MRPL11, S100A6, RBM4, SLC39A1, FAU PC 3 Positive: WNT6, FARSB, USP37, ACSL3, WDFY1, MRPL44, TMBIM1, SERPINE2, PNKD, CUL3 AAMP, MFF, AGFG1, ARPC2, PID1, TRIP12, CAB39, IGFBP2, ITM2C, PSMD1 RPL37A, NCL, PTMA, XRCC5, DIS3L2, EIF4E2, MREG, GIGYF2, DGKD, LINC00607 Negative: CGA, ZNF292, RARS2, ORC3, AKIRIN2, RNGTT, SNHG5, PNRC1, UBE2J1, SYNCRIP LYRM2, SNX14, MDN1, PGM3, UBE3D, CASP8AP2, TPBG, UFL1, TTK, NDUFAF4 ELOVL4, MMS22L, SH3BGRL2, PNISR, HMGN3, USP45, PHIP, CCNC, MYO6, ASCC3 PC 4 Positive: RHOG, RRM1, PGAP2, NUP98, TRIM5, ZNF195, CARS, CCKBR, NAP1L4, ARFIP2 PHLDA2, TIMM10B, CDKN1C, KCNQ1OT1, TSSC4, ILK, CD81, H19, TAF10, MRPL23 CTSD, MRPL17, MOB2, PPFIBP2, AP2A2, EIF3F, CHID1, NUMA1, RNF121, DHCR7 Negative: RNF34, KDM2B, ANAPC5, C12orf43, ORAI1, SPPL3, MLEC, TMEM120B, POP5, PSMD9 RNF10, DYNLL1, VPS33A, SRSF9, CLIP1, GATC, TRIAP1, ZCCHC8, COX6A1, RSRC2 PXN, DENR, RPLP0, RAB35, ARL6IP4, HSPB8, SUDS3, PITPNM2, TAOK3, PEBP1 PC 5 Positive: ABCF1, PPP1R10, GNL1, MRPS18B, DHX16, HLA-E, TUBB, RPP21, FLOT1, PPP1R11 IER3, POU5F1, TRIM27, HLA-C, HIST1H1B, DDX39B, HIST1H2AH, BAG6, ABT1, GPANK1 HMGN4, CSNK2B, HIST1H1D, CLIC1, HIST1H1E, VARS, HIST1H4C, HIST1H1C, LSM2, HIST1H3B Negative: PPFIBP2, EIF3F, MRPL17, RPL27A, TAF10, TMEM9B, ILK, DENND5A, TIMM10B, TMEM41B ARFIP2, IPO7, CCKBR, ZNF143, TRIM5, RRM1, WEE1, RHOG, SWAP70, PGAP2 SBF2, NUP98, ADM, AMPD3, ZNF195, MTRNR2L8, CARS, CTR9, NAP1L4, EIF4G2 Computing nearest neighbor graph Computing SNN INFO [2022-12-09 16:50:26] define_signif_tumorsubclusters(), tumor: 1 Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |=====================================================================================| 100% PC 1 Positive: KIAA1217, PIP4K2A, ARHGAP21, BMI1, ABI1, DNAJC1, YME1L1, MLLT10, RAB18, NEBL MPP7, UBE2H, MEST, NRF1, MKLN1, AHCYL2, PODXL, CHCHD3, WAC, EXOC4 TNPO3, PLXDC2, SLC35B4, ATP6V1F, AKR1B1, CALU, CALD1, BAMBI, CNOT4, METTL2B Negative: RPS11, NOSIP, IRF3, BCL2L12, RPL13A, PRMT1, AP2A1, PIH1D1, PTOV1, SNRNP70 AKT1S1, NUP62, CGB7, ATF5, CGB8, NR1H2, EMC10, CGB5, RUVBL2, C19orf48 GYS1, ETFB, FTL, BAX, PPP2R1A, NUCB1, ZNF480, PPP1R15A, RPL18, ZNF808 PC 2 Positive: TEAD1, LINC00958, BTBD10, RPL27A, TMEM9B, PARVA, DENND5A, EIF3F, TMEM41B, IPO7 FAR1, MICAL2, ZNF143, USP47, EIF4G2, WEE1, RRAS2, PPFIBP2, SWAP70, MRPL17 CTR9, COPB1, TAF10, SBF2, PSMA1, ILK, ADM, AMPD3, MTRNR2L8, TIMM10B Negative: S100A14, S100A16, S100A6, S100A13, PRR9, CHTOP, S100A11, S100A10, ILF2, MRPL9 GATAD2B, SLC39A1, SNX27, JTB, POGZ, RAB13, PSMB4, RPS27, PSMD4, TPM3 C1orf43, PIP5K1A, UBAP2L, VPS72, HAX1, SCNM1, ADAR, MLLT11, APOA1, SHC1 PC 3 Positive: DPPA5, KHDC3L, KHDC1L, OOEP, EEF1A1, SMAP1, COX7A2, FAM135A, TMEM30A, PHF3 SENP6, MYO6, PRIM2, PHIP, BAG2, HMGN3, ZNF451, SH3BGRL2, ELOVL4, DST TTK, COL21A1, TPBG, LRRC1, UBE3D, GCLC, PGM3, ELOVL5, SNX14, GCM1 Negative: BIN2, SMAGP, SLC4A8, DAZAP2, KRT80, TFCP2, KRT7, SLC11A2, KRT8, ATF1 KRT18, DIP2B, LARP4, EIF4B, LIMA1, PFDN5, CERS5, C12orf10, COX14, PRR13 SMARCD1, PCBP2, MAP3K12, RACGAP1, CBX5, CCT3, TMBIM6, HNRNPA1, SMG5, COPZ1 PC 4 Positive: DYRK1A, PSMG1, BRWD1, TTC3, HLCS, MORC3, HMGN1, CBR1, MX1, RUNX1 WDR4, SLC5A3, NDUFV3, MRPS6, ITSN1, ERVH48-1, DONSON, PKNOX1, SON, GART TMEM50B, RRP1B, PAXBP1, SYNJ1, PDXK, MIS18A, SOD1, CSTB, TIAM1, BACH1 Negative: SNHG5, CGA, SYNCRIP, SNX14, PGM3, ZNF292, UBE3D, RARS2, ORC3, TPBG NDUFAF4, AKIRIN2, UFL1, MMS22L, CASP8AP2, RNGTT, PNISR, MDN1, TTK, PNRC1 UBE2J1, LYRM2, USP45, ELOVL4, CCNC, ASCC3, SH3BGRL2, LIN28B, PREP, ATG5 PC 5 Positive: NDUFC1, ELF2, SLC7A11, SCLT1, NAA15, PGRMC2, LARP1B, SETD7, SPATA5, CCNA2 MGST2, EXOSC9, MAML3, ANXA5, SCOC, PRDM5, ZNF330, MAD2L1, GAB1, SMARCA5 C4orf3, ANAPC10, ABCE1, LSM6, USP53, SLC10A7, ARHGAP10, SEC24D, LRBA, RPS3A Negative: THOC3, SIMC1, SFXN1, NOP16, MSX2, CPEB4, BOD1, STC2, HIGD2A, ATP6V0E1 RPL26L1, CLTB, SH3PXD2B, UBTD2, FAF2, STK10, FBXW11, UIMC1, NPM1, RANBP17 NSD1, SPDL1, PANK3, PRELID1, RARS, LMAN2, TMED9, WWC1, N4BP3, NHP2 Computing nearest neighbor graph Computing SNN INFO [2022-12-09 16:50:28] define_signif_tumorsubclusters(), tumor: 2 Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |=====================================================================================| 100% PC 1 Positive: FTL, GYS1, BAX, RUVBL2, CGB5, CGB8, PIH1D1, SNRNP70, NUCB1, CGB7 RPL13A, RPS11, NOSIP, PPP1R15A, RPL18, IRF3, GRWD1, BCL2L12, NAPA, ZNF114 SAE1, KDELR1, ZC3H4, PRMT1, TMEM160, AP2S1, AP2A1, SLC1A5, PTOV1, CALM3 Negative: STK24, DOCK9, FARP1, UBAC2, IPO5, TM9SF2, PCCA, MBNL2, TPP2, UGGT2 TEX30, DNAJC3, ARGLU1, GPC6, COL4A1, NDFIP2, COL4A2, CARS2, RBM26, ING1 EDNRB, ANKRD10, MYCBP2, ARHGEF7, FBXL3, TUBGCP3, CLN5, ATP11A, LMO7, UCHL3 PC 2 Positive: RFC3, ALG5, PDS5B, N4BP2L2, EXOSC8, UFM1, HSPH1, PROSER1, HMGB1, COG6 UBL3, POMP, MRPS31, PAN3, POLR1D, ELF1, LNX2, MTIF3, WBP4, GTF3A VWA8, RPL21, DNAJC15, CDK8, TSC22D1, RNF6, NUFIP1, ATP8A2, GTF2F2, MTMR6 Negative: TRIO, DAP, ZNF622, MARCH6, MYO10, CCT5, NSUN2, MED10, BASP1, IRX2 IRX4, C5orf17, NDUFS6, GOLPH3, MRPL36, MTMR12, LPCAT1, CLPTM1L, ZFR, TRIP13 BRD9, PDCD6, SDHA, PLEKHG4B, SUB1, TARS, RAI14, EPB41L3, ARHGAP28, RAD1 PC 3 Positive: B4GALNT3, KDM5A, WNK1, ERC1, ADIPOR2, FKBP4, FOXM1, TEAD4, TSPAN9, RAD51AP1 NDUFA9, CD9, TNFRSF1A, LTBR, MRPL51, GAPDH, NOP2, CHD4, MLF2, PTMS CDCA3, TPI1, LRRC23, C12orf57, EMG1, PHB2, LPCAT3, DPPA3, NANOG, SLC2A3 Negative: LGMN, RIN3, CPSF2, GOLGA5, NDUFB1, BTBD7, ATXN3, TRIP11, DDX24, RPS6KA5 GLRX5, TTC7B, GSKIP, PAPOLA, CALM1, PSMC1, VRK1, TDP1, SETD3, EFCAB11 CCNK, FOXN3, YY1, ZC3H14, MEG3, MSX2, CPEB4, CEP128, SFXN1, FAM193A PC 4 Positive: LYRM2, MDN1, CASP8AP2, UBE2J1, PNRC1, UFL1, RNGTT, NDUFAF4, AKIRIN2, MMS22L ORC3, PNISR, RARS2, USP45, ZNF292, CCNC, CGA, ASCC3, SNHG5, SYNCRIP LIN28B, SNX14, PREP, PGM3, UBE3D, ATG5, TPBG, TTK, QRSL1, ELOVL4 Negative: ORMDL2, PMEL, SARNP, GDF11, CDK2, CD63, RAB5B, BLOC1S1, RPS26, ERBB3 GTSF1, PA2G4, ITGA5, COPZ1, RPL41, HNRNPA1, MYL6B, CBX5, MYL6, MAP3K12 SMARCC2, PCBP2, RNF41, PRR13, CNPY2, C12orf10, RBMS2, PFDN5, BAZ2A, EIF4B PC 5 Positive: PFDN5, C12orf10, PRR13, EIF4B, PCBP2, KRT18, KRT8, MAP3K12, CBX5, KRT7 KRT80, HNRNPA1, SLC4A8, COPZ1, BIN2, ITGA5, SMAGP, GTSF1, DAZAP2, BLOC1S1 TFCP2, CD63, SLC11A2, GRWD1, RPL18, PTDSS1, UQCRB, KDELR1, MTDH, LAPTM4B Negative: PUS1, SFSWAP, RAN, BRI3BP, GTF2H3, DHX37, NCOR2, EP400, UBC, EIF2B1 DDX55, POLE, TMED2, PXMP2, RILPL1, PGAM5, SNRNP35, ANKLE2, RILPL2, ZNF195 CARS, NUP98, NAP1L4, SBNO1, GOLGA3, PGAP2, PHLDA2, RHOG, CDKN1C, CHFR Computing nearest neighbor graph Computing SNN INFO [2022-12-09 16:50:29] define_signif_tumorsubclusters(), tumor: 3 Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |=====================================================================================| 100% PC 1 Positive: UCHL3, COMMD6, TBC1D4, LMO7, CLN5, KLF5, MZT1, PIBF1, DIS3, LINC00383 FBXL3, TDRD3, MYCBP2, DIAPH3, EDNRB, LINC00458, RBM26, SUGT1, NDFIP2, GPC6 CKAP2, DNAJC3, VPS36, UGGT2, ATP7B, MBNL2, WDFY2, IPO5, SWT1, IVNS1ABP Negative: RPS28, NDUFA7, CD320, ELAVL1, HNRNPM, TIMM44, ZNF121, PET100, TRAPPC5, INSR TRIP10, UBL5, TUBB4A, KHSRP, GTF2F1, ALKBH7, PIN1, CLPP, MLLT1, NDUFA11 PPAN, RPS26, LONP1, ERBB3, PA2G4, RPL41, RPL36, TGFB1, EXOSC5, HNRNPUL1 PC 2 Positive: KPNA6, KHDRBS1, TXLNA, PTP4A2, EIF3I, TINAGL1, HDAC1, ZBTB8OS, MARCKSL1, RBBP4 SYNC, ZCCHC17, YARS, TMEM54, RNF19B, SNRNP40, AK2, PHC2, SMIM12, SFPQ PUM1, ZMYM4, PSMB2, CLSPN, SRSF4, AGO1, AGO3, EPB41, TRAPPC3, MAP7D1 Negative: NDUFC1, ELF2, SLC7A11, SCLT1, PGRMC2, LARP1B, SPATA5, CCNA2, EXOSC9, SH3D19 ANXA5, PRDM5, FAM160A1, FBXW7, MAD2L1, TMEM154, C4orf3, ARFIP1, FHDC1, USP53 SEC24D, TRIM2, SNHG8, CAMK2D, PLRG1, ANK2, LARP7, PPID, ENPEP, ELOVL6 PC 3 Positive: MTAP, FOCAD, RPS6, CAAP1, DENND4C, PLAA, PLIN2, HAUS6, RRAGA, PSIP1 SNAPC3, MPDZ, RUFY1, HNRNPH1, KDM4C, CANX, HNRNPAB, NHP2, GLDC, MGAT4B N4BP3, SQSTM1, TMED9, LMAN2, PRELID1, UIMC1, NSD1, UHRF2, FAF2, TBC1D9B Negative: TRIML2, SLC25A4, ZFP42, UFSP2, FRG1, CASP3, RWDD4, ING2, DCTD, WWC2 TENM3, AC078881.1, SPCS3, HPGD, NDUFC1, ANK2, LARP7, ENPEP, CAMK2D, HMGB2 ELOVL6, ELF2, SNHG8, GAR1, SLC7A11, SEC24D, AADAT, SCLT1, PLA2G12A, ANXA5 PC 4 Positive: ZFR, SUB1, MTMR12, GOLPH3, TARS, C5orf17, RAI14, RAD1, BASP1, MYO10 BRIX1, ZNF622, TRIO, DAP, MARCH6, CCT5, NSUN2, MED10, IRX2, IRX4 NDUFS6, MRPL36, MYL12B, LPCAT1, MYL12A, CLPTM1L, LPIN2, TRIP13, SMCHD1, BRD9 Negative: NDUFC1, ELF2, SLC7A11, SCLT1, PGRMC2, SH3D19, LARP1B, SPATA5, FAM160A1, CCNA2 FBXW7, TMEM154, EXOSC9, ARFIP1, ANXA5, FHDC1, PRDM5, TRIM2, MAD2L1, PLRG1 C4orf3, PPID, USP53, FNIP2, SEC24D, RAPGEF2, NAF1, TMA16, SNHG8, MSMO1 PC 5 Positive: EXOSC4, MAF1, CYC1, GRINA, MROH1, PLEC, BOP1, HSF1, SLC52A2, JAM3 ZBTB44, APLP2, VPS28, THYN1, ST3GAL4, ARHGAP32, CHEK1, RPL8, STT3A, C8orf33 EI24, HMGN1, TTC3, HLCS, DYRK1A, PSMG1, BRWD1, MORC3, CBR1, RUNX1 Negative: SNRPA1, TM2D3, CHSY1, IGF1R, CHD2, NR2F2, MEF2A, PRC1, UNC45A, FURIN BLM, CRTC3, IQGAP1, NGRN, IDH2, FANCI, AEN, WIPI2, SDK1, TNRC18 MRPS11, ACTB, FSCN1, GNA12, CAMK2N1, RNF216, MRPL46, CHST12, OTUD3, AIMP2 Computing nearest neighbor graph Computing SNN INFO [2022-12-09 16:50:30] define_signif_tumorsubclusters(), tumor: 4 Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |=====================================================================================| 100% PC 1 Positive: C19orf48, ETFB, EMC10, PPP2R1A, NR1H2, ZNF480, ATF5, NUP62, AKT1S1, ZNF808 PTOV1, AP2A1, PRMT1, ZNF83, BCL2L12, IRF3, ZNF611, NOSIP, RPS11, ZNF600 RPL13A, PIH1D1, SNRNP70, CGB7, ZNF28, CGB8, CGB5, RUVBL2, GYS1, ZNF468 Negative: UBE2D3, CISD2, CENPE, TET2, MANBA, PPA2, INTS12, PPP3CA, GSTCD, H2AFZ TBCK, DNAJB14, AIMP1, LAMTOR3, GOLPH3L, CERS2, ENSA, PAPSS1, C1orf56, CDC42SE1 MLLT11, MCL1, SCNM1, VPS72, RPRD2, TRMT10A, PIP5K1A, HADH, PRPF3, PSMD4 PC 2 Positive: NUCB2, PIK3C2A, ZDHHC13, SPTY2D1, SAA1, LDHA, GTF2H1, E2F8, TSG101, RPS13 PLEKHA7, C11orf58, CALCB, PSMA1, COPB1, RRAS2, FAR1, BTBD10, LINC00958, MPHOSPH8 PSPC1, TEAD1, ZMYM2, AL161772.1, PARVA, ARID3A, XPO4, SAP18, PTBP1, LATS2 Negative: KLF10, UBR5, AZIN1, RRM2B, GRHL2, ZNF706, ATP6V1C1, YWHAZ, CTHRC1, PABPC1 RNF19A, POLR2K, DCAF13, COX6C, VPS13B, STK3, ZFPM2, RPL30, LAPTM4B, MTDH OXR1, PTDSS1, UQCRB, EIF3E, NDUFAF6, ESRP1, EMC2, OTUD6B, NUDCD1, RIPK2 PC 3 Positive: SDC4, STK4, SYS1, TOMM34, DBNDD2, DNTTIP1, YWHAB, PKIG, UBE2C, SERINC3 PLTP, SLC35C2, TP53RK, ZMYND8, NCOA3, PREX1, ARFGEF2, CSE1L, STAU1, DDX27 ZFAS1, B4GALT5, RNF114, UBE2V1, TMEM189, CEBPB, PTPN1, PARD6B, ADNP, DPM1 Negative: XPNPEP3, RBX1, ST13, SLC25A17, EP300, ADSL, L3MBTL2, TNRC6B, RANGAP1, RPS19BP1 TOB2, ATF4, MIEF1, PHF5A, ACO2, SYNGR1, POLR3H, RPL3, PMM1, TOMM22 DDX17, DESI1, CSNK1E, TMEM184B, XRCC6, MAFF, SREBF2, POLR2F, MICALL1, SMDT1 PC 4 Positive: RPS26, ERBB3, PA2G4, RAB5B, RPL41, CDK2, MYL6B, PMEL, MYL6, ORMDL2 SMARCC2, SARNP, RNF41, GDF11, CNPY2, CD63, RBMS2, BLOC1S1, BAZ2A, GTSF1 ITGA5, PTGES3, COPZ1, NACA, HNRNPA1, PRIM1, CBX5, LRP1, MAP3K12, PCBP2 Negative: GNAS, NELFCD, VAPB, CTSZ, TAF4, RAB22A, PSMA7, RBM38, MTG2, RPS25 HYOU1, HMBS, CCDC84, BCL9L, H2AFX, DDX6, RAE1, ARCN1, CBL, OSBPL2 KMT2A, MCAM, UBE4A, BMP7, ADRM1, RNF214, PCSK7, ARHGEF12, TAGLN, TFAP2C PC 5 Positive: COPZ1, HNRNPA1, ITGA5, GTSF1, CBX5, BLOC1S1, ERBB3, CD63, GDF11, RPS26 PA2G4, SARNP, MAP3K12, RAB5B, ORMDL2, PMEL, CDK2, PCBP2, RPL41, PRR13 MYL6B, C12orf10, PFDN5, MYL6, EIF4B, KRT7, KRT18, KRT8, KRT80, SLC4A8 Negative: SH3GL1, CHAF1A, MAP2K2, ZBTB7A, DPP9, PLIN3, EEF2, DAPK3, SAFB2, MRPL54 PIP5K1C, SAFB, HMG20B, MFSD12, RPL36, DOHH, LONP1, NCLN, THOP1, NDUFA11 SGTA, MLLT1, SLC39A3, CLPP, GADD45B, ALKBH7, LMNB2, GTF2F1, TIMM13, ETFA Computing nearest neighbor graph Computing SNN INFO [2022-12-09 16:50:32] define_signif_tumorsubclusters(), tumor: doublet Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |=====================================================================================| 100% PC 1 Positive: SLC39A3, SGTA, GADD45B, THOP1, LMNB2, NCLN, TIMM13, DOHH, LSM7, MFSD12 OAZ1, HMG20B, PLEKHJ1, PIP5K1C, AP3D1, MKNK2, MRPL54, CSNK1G2, DAPK3, ABHD17A TCF3, EEF2, UQCR11, ZBTB7A, MBD3, MAP2K2, MEX3D, RPS15, SH3GL1, DAZAP1 Negative: NCKAP1, NUP35, DNAJC10, UBE2E3, CWC22, ZC3H15, SESTD1, AC007319.1, AGPS, NFE2L2 TFPI, HNRNPA3, MTX2, GULP1, CIR1, OLA1, SP3, ITGA6, WDR75, HAT1 DYNC1I2, DCAF17, METTL8, TLK1, GORASP2, UBR3, METTL5, SSB, KLHL23, SLC40A1 PC 2 Positive: NUP107, SLC35E3, RAP1B, MDM2, CAND1, CPM, GRIP1, TMBIM4, LLPH, CPSF6 RASSF3, TBK1, XPOT, YEATS4, SRGAP1, FRS2, PPM1H, CCT2, MON2, RAB3IP USP15, CNOT2, TSFM, ZFC3H1, RAB21, METTL1, TBC1D15, CDK4, TRHDE, KRR1 Negative: EEF1B2, FASTKD2, NDUFS1, CREB1, CCNYL1, RPE, INO80D, BARD1, FZD5, IDH1 ATIC, RAPH1, FN1, ABI2, CYP20A1, LINC00607, NBEAL1, MREG, XRCC5, WDR12 RPL37A, BMPR2, IGFBP2, NOP58, ARPC2, SUMO1, AAMP, NDUFB3, PNKD, ORC2 PC 3 Positive: MLEC, POP5, SPPL3, RNF10, C12orf43, DYNLL1, ANAPC5, RNF34, SRSF9, KDM2B ORAI1, GATC, TMEM120B, TRIAP1, PSMD9, COX6A1, VPS33A, PXN, CLIP1, RPLP0 ZCCHC8, RAB35, RSRC2, HSPB8, DENR, ARL6IP4, SUDS3, RIMKLB, A2ML1-AS1, SLC2A3 Negative: ODC1, HPCAL1, NOL10, RRM2, GRHL1, ATP6V1C2, TAF1B, YWHAQ, PDIA6, ADAM17 ROCK2, IAH1, NBAS, CPSF3, ITGB1BP1, DDX1, ID2, MYCN, RPS7, RNASEH1 FAM49A, TMEM41B, ADI1, IPO7, DENND5A, ZNF143, TMEM18, TMEM9B, WEE1, ACP1 PC 4 Positive: HIST1H3B, HIST1H1A, HIST1H1C, GMNN, HIST1H4C, C6orf62, HIST1H1E, ACOT13, HIST1H1D, TDP2 HMGN4, MRS2, CASC15, ABT1, SOX4, HIST1H2AH, CDKAL1, HIST1H1B, E2F3, TRIM27 DEK, TPMT, PPP1R11, KIF13A, RPP21, NUP153, HLA-E, CAP2, GNL1, DTNBP1 Negative: FGFR2, ATE1, NSMCE4A, TACC2, BUB3, OAT, ZRANB1, CTBP2, BCCIP, DHX32 RILPL1, SNRNP35, TMED2, EIF2B1, DDX55, RILPL2, DOCK1, GTF2H3, SBNO1, NCOR2 CDK2AP1, PITPNM2, ARL6IP4, DENR, UBC, RSRC2, ZCCHC8, CLIP1, DHX37, PTPRE PC 5 Positive: SNRNP70, CGB7, CGB8, CGB5, ATF5, RUVBL2, NR1H2, GYS1, EMC10, FTL C19orf48, BAX, NUCB1, ETFB, PPP1R15A, RPL18, PPP2R1A, GRWD1, KDELR1, ZNF480 ZNF114, ZNF808, NAPA, SAE1, ZNF83, ZC3H4, TMEM160, ZNF611, AP2S1, SLC1A5 Negative: NOL7, TBC1D7, RANBP9, HIVEP1, MCUR1, JARID2, SMIM13, DTNBP1, TMEM14B, CAP2 NUP153, TMEM14C, KIF13A, PAK1IP1, TPMT, DEK, GCNT2, PRRC2B, E2F3, NUP214 RAPGEF1, AIF1L, MED27, SETX, ABL1, TFAP2A, DDX31, GTF3C4, FUBP3, SURF6 Computing nearest neighbor graph Computing SNN INFO [2022-12-09 16:50:33] define_signif_tumor_subclusters(), tumor: unassigned INFO [2022-12-09 16:50:33] Less cells in group unassigned than k_nn setting. Keeping as a single subcluster. Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |=====================================================================================| 100% Error in irlba(A = t(x = object), nv = npcs, ...) : max(nu, nv) must be strictly less than min(nrow(A), ncol(A))