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!

Hello,

the first argument of genCountMatrixFromVcf needs to be a BSgenome object, not a string, like this:

library(BSgenome.Hsapiens.UCSC.hg19)

m0 = genCountMatrixFromVcf(BSgenome.Hsapiens.UCSC.hg19, vo)