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Running trinucleotideMatrix generates Error in.Call2
Hi, While running, I got a mistake, like`
laml.tnm = trinucleotideMatrix(maf = maf,ref_genome = "BSgenome.Hsapiens.UCSC.hg38")
-Extracting 5' and 3' adjacent bases
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord, :
solving row 32714: 'allow.nonnarrowing' is FALSE and the supplied start (242366418) is > refwidth + 1`.
sessionInfo
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome.Hsapiens.UCSC.hg38_1.4.5
[3] BSgenome_1.70.1 rtracklayer_1.62.0
[5] BiocIO_1.12.0 Biostrings_2.70.1
[7] XVector_0.42.0 GenomicRanges_1.54.1
[9] GenomeInfoDb_1.38.5 IRanges_2.36.0
[11] S4Vectors_0.40.2 BiocGenerics_0.48.1
[13] maftools_2.16.0
loaded via a namespace (and not attached):
[1] Matrix_1.6-4 compiler_4.3.1 rjson_0.2.21
[4] crayon_1.5.2 SummarizedExperiment_1.32.0 Biobase_2.62.0
[7] Rsamtools_2.18.0 bitops_1.0-7 GenomicAlignments_1.38.0
[10] parallel_4.3.1 splines_4.3.1 BiocParallel_1.36.0
[13] yaml_2.3.8 lattice_0.22-5 DNAcopy_1.76.0
[16] S4Arrays_1.2.0 XML_3.99-0.16 DelayedArray_0.28.0
[19] MatrixGenerics_1.14.0 GenomeInfoDbData_1.2.11 RColorBrewer_1.1-3
[22] SparseArray_1.2.3 zlibbioc_1.48.0 grid_4.3.1
[25] rstudioapi_0.15.0 data.table_1.15.2 codetools_0.2-19
[28] survival_3.5-7 abind_1.4-5 RCurl_1.98-1.13
[31] restfulr_0.0.15 matrixStats_1.2.0 tools_4.3.1
Because I am using Homo_sapiens. GRCh38. DNA. Primary_assembly
annotations, so I think should use GRCh38 in trinucleotideMatrix function.
Do you have any suggestion how to solve it? Thanks Olsen