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TRASA
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@trasa-17881
Last seen 5.4 years ago
Hi all
I have a list of VCF files, where I would like to assess the mutational signature from. First, I needed to combine the vcf's in one matrix according to signeR vignette.
mut = matrix(ncol=96,nrow=0)
for(i in list_vcf) {
vo = readVcf(i, "hg19")
# sample name (should pick up from the vcf automatically if available)
# colnames(vo) = i
m0 = genCountMatrixFromVcf("BSgenome.Hsapiens.UCSC.hg19", vo)
mut = rbind(mut, m0)
}
When I run this, I get following error message
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘getSeq’ for signature ‘"character"’
Has anyone come across the same problem and can help me to resolve this?
My sessioninfo
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome_1.50.0 rtracklayer_1.42.2 signeR_1.8.0 NMF_0.21.0 cluster_2.0.9
[6] rngtools_1.3.1 pkgmaker_0.27 registry_0.5-1 VariantAnnotation_1.28.13 Rsamtools_1.34.1
[11] Biostrings_2.50.2 XVector_0.22.0 SummarizedExperiment_1.12.0 DelayedArray_0.8.0 BiocParallel_1.16.6
[16] matrixStats_0.54.0 Biobase_2.42.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 IRanges_2.16.0
[21] S4Vectors_0.20.1 BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] httr_1.4.0 bit64_0.9-7 foreach_1.4.4 assertthat_0.2.1 BiocManager_1.30.4
[6] blob_1.1.1 GenomeInfoDbData_1.2.0 yaml_2.2.0 progress_1.2.1 pillar_1.4.0
[11] RSQLite_2.1.1 lattice_0.20-38 glue_1.3.1 digest_0.6.18 RColorBrewer_1.1-2
[16] colorspace_1.4-1 Matrix_1.2-17 plyr_1.8.4 XML_3.98-1.19 pkgconfig_2.0.2
[21] bibtex_0.4.2 biomaRt_2.38.0 zlibbioc_1.28.0 purrr_0.3.2 xtable_1.8-4
[26] scales_1.0.0 tibble_2.1.1 ggplot2_3.1.1 withr_2.1.2 GenomicFeatures_1.34.8
[31] lazyeval_0.2.2 magrittr_1.5 crayon_1.3.4 memoise_1.1.0 doParallel_1.0.14
[36] class_7.3-15 PMCMR_4.3 tools_3.5.1 prettyunits_1.0.2 hms_0.4.2
[41] gridBase_0.4-7 stringr_1.4.0 munsell_0.5.0 AnnotationDbi_1.44.0 compiler_3.5.1
[46] rlang_0.3.4 nloptr_1.2.1 grid_3.5.1 RCurl_1.95-4.12 iterators_1.0.10
[51] rstudioapi_0.10 bitops_1.0-6 gtable_0.3.0 codetools_0.2-16 DBI_1.0.0
[56] reshape2_1.4.3 R6_2.4.0 GenomicAlignments_1.18.1 dplyr_0.8.0.1 bit_1.1-14
[61] stringi_1.4.3 Rcpp_1.0.1 tidyselect_0.2.5
Thanks!