How can I use a vcf file in trackViewer? Issues with TabixFile - coercing S4 class to a vector
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9 weeks ago

Hello, I am trying to use TrackViewer to generate a lollipop plot for mutations annotated in a vcf file format. I am pretty bad at R and cannot get past the vcf itself! I've not found how to get by this step. Thanks

Example vcf (no quality info available):

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
2   60553260    mbsb    C   A           
2   60546217    shcd    T   G           

What I have tried:

vcf.fl <- VariantAnnotation::readVcf(file = "test.vcf", genome = "hg38")
tab <- TabixFileList(vcf.fl, index=paste(vcf.fl, "tbi", sep="."))
Error in as.vector(x, mode = "character") : 
  no method for coercing this S4 class to a vector



gr <- GRanges("2", IRanges(60457194, 60553654, names="BCL11A"))
vcf <- readVcf(vcf.fl, "hg38", param=gr)
Error in (function (classes, fdef, mtable)  : 
#unable to find an inherited method for function 'readVcf' for signature '"CollapsedVCF", "GRanges"'


sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] rtracklayer_1.48.0          Gviz_1.32.0                 maftools_2.4.12            
 [4] VariantAnnotation_1.34.0    Rsamtools_2.4.0             Biostrings_2.56.0          
 [7] XVector_0.28.0              SummarizedExperiment_1.18.2 DelayedArray_0.14.1        
[10] matrixStats_0.58.0          Biobase_2.48.0              GenomicRanges_1.40.0       
[13] GenomeInfoDb_1.24.2         IRanges_2.22.2              S4Vectors_0.26.1           
[16] BiocGenerics_0.37.0   
vcf R VariantAnnotation trackViewer • 171 views
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