Entering edit mode
2.9 years ago
cristinadias.gen
▴
10
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