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Inferring CNV from Single-Cell RNA-Seq
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Error in m[match(oldnodes, m)] <- 1:(N - 1) : NAs are not allowed in subscripted assignments #624

Closed biobirds9 closed 9 months ago

biobirds9 commented 9 months ago

Thank you for your efforts with inferCNV. I am submitting my assignment through the following command:

infercnv

Everything seems to be fine, but I'm getting the following error, and I can't find the reason for it, so I'd appreciate your help!

_Computing nearest neighbor graph Computing SNN Error in m[match(oldnodes, m)] <- 1:(N - 1) : NAs are not allowed in subscripted assignments Calls: ... .single_tumor_leidensubclustering -> as.hclust -> as.hclust.phylo Execution halted

DylanGuo1101 commented 3 months ago

I encountered the same issue, have you solved it? Thank you!

    STEP 15: computing tumor subclusters via leiden

INFO [2024-05-19 22:13:41] define_signif_tumor_subclusters(p_val=0.1
INFO [2024-05-19 22:13:45] define_signif_tumor_subclusters(), tumor: T_hep
INFO [2024-05-19 22:13:49] Setting auto leiden resolution for T_hep to 0.000736312
Warning: Data is of class matrix. Coercing to dgCMatrix.
Finding variable features for layer counts
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:  RELL1, PGM2, TBC1D1, C4orf19, KLF3, ARAP2, FAM114A1, KLHL5, WDR19, STIM2 
       RFC1, TBC1D19, KLB, RBPJ, LIAS, SMIM20, UGDH, ANAPC4, UGDH-AS1, PI4K2B 
       SMIM14, UBE2K, SEPSECS, PDS5A, DHX15, N4BP2, PPARGC1A, GBA3, RBM47, ADGRA3 
Negative:  TECR, ILVBL, NDUFB7, BRD4, GIPC1, PKN1, AKAP8L, DDX39A, PRKACA, PGLYRP2 
       C19orf53, CYP4F2, CYP4F12, CYP4F3, CYP4F11, CCDC130, TPM4, STX10, RAB8A, FAM32A 
       NFIX, AP1M1, EPS15L1, GADD45GIP1, CHERP, SLC35E1, RAD23A, SMIM7, MYO9B, CALR 
PC_ 2 
Positive:  NCOA2, ARFGEF1, CSPP1, SGK3, TRAM1, VCPIP1, COPS5, SNHG6, LACTB2, ADHFE1 
       TERF1, RRS1, RDH10, TRIM55, STAU2, PDE7A, MTFR1, UBE2W, ARMC1, ELOC 
       CYP7B1, TMEM70, YTHDF3, MIR2052HG, TTPA, HNF4G, GGH, ASPH, ZFHX4, CHD7 
Negative:  POLR2J, POLR2J3, PRKRIP1, ARMC10, CUX1, NAPEPLD, IFT22, PMPCB, FIS1, CLDN15 
       PSMC2, ZNHIT1, PLOD3, ORC5, MOGAT3, AP1S1, KMT2E-AS1, SERPINE1, TRIM56, SRRT 
       KMT2E, TRIP6, POP7, GNB2, TFR2, SRPK2, MOSPD3, PCOLCE, AGFG2, TSC22D4 
PC_ 3 
Positive:  C20orf194, ITPA, ATRN, C20orf27, DDRGK1, CDC25B, MRPS26, MAVS, PANK2, PRNP 
       SLC23A2, TMEM230, PCNA, CDS2, GPCPD1, TRMT6, SPTLC3, TASP1, SLX4IP, ESF1 
       MKKS, NDUFAF5, MACROD2, CRLS1, PLCB1, TMX4, KIF16B, HAO1, SNRPB2, POFUT1 
Negative:  ANGPTL3, ATG4C, ALG6, ITGB3BP, DOCK7, PGM1, USP1, JAK1, AK4, LEPROT 
       TM2D1, LEPR, SGIP1, SLC35D1, MIER1, NFIA, SERBP1, CYP2J2, GADD45A, GNG12 
       HOOK1, GNG12-AS1, FGGY, MYSM1, OMA1, LRRC40, DAB1, C8B, C8A, SRSF11 
PC_ 4 
Positive:  PRKAR2A, IP6K2, SLC25A20, UQCRC1, SHISA5, PLXNB1, ARIH2, TMA7, NME6, MAP4 
       DHX30, SMARCC1, P4HTM, ELP6, SCAP, KIF9, SETD2, WDR6, CCDC12, TDGF1 
       DALRD3, LSM14A, KIAA0355, PEPD, GPI, CEBPG, UBA2, NDUFAF3, CEBPA, SCGB2B2 
Negative:  TFPI, WDR75, SLC40A1, AC007319.1, ASNSD1, ITGAV, ZC3H15, NCKAP1, ANKAR, UBE2E3 
       CWC22, ZNF385B, SESTD1, ORMDL1, PLEKHA3, PMS1, FKBP7, C2orf88, PRKRA, HIBCH 
       INPP1, AGPS, NAB1, GLS, NFE2L2, STAT1, STAT4, MYO1B, HNRNPA3, GTF3C3 
PC_ 5 
Positive:  ACAA1, CTDSPL, NISCH, PDCD6IP, CLASP2, GLYCTK, UBP1, CRTAP, WDR82, GLB1 
       TWF2, CNOT10, ALAS1, DYNC1LI1, CMTM6, ACY1, ABHD14A, CMTM8, STT3B, ABHD14B 
       RRP9, TGFBR2, TEX264, AZI2, RAD54L2, MANF, CMC1, HEMK1, TMEM115, TDGF1 
Negative:  USF2, LSR, TMEM147, FXYD5, RBM42, FXYD1, HPN, COX6B1, GRAMD1A, U2AF1L4 
       ZNF599, ZNF181, PSENEN, ZNF302, PRODH2, TYROBP, SCGB2B2, SDHAF1, UBA2, POLR2I 
       TBCB, GPI, CAPNS1, KIAA0355, COX7A1, LSM14A, ZNF565, ZNF146, PEPD, LINC00665 
Computing nearest neighbor graph
Computing SNN
Error in m[match(oldnodes, m)] <- 1:(N - 1) : 
  NAs are not allowed in subscripted assignments
zjh19950218 commented 2 days ago

options(scipen = 100), the reason you can refer to https://github.com/broadinstitute/infercnv/issues/396#:~:text=Here%20are%20the%20commands%20I%20have%20run:%20infercnv_obj