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Simon-Coetzee / motifBreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
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Variants From File Documentation Missing #24

Open DarioS opened 4 years ago

DarioS commented 4 years ago

Trying to open it results in an error message.

> ?variants.from.file
No documentation for 'variants.from.file' in specified packages and libraries

However, ?snps.from.file works just fine and opens the documentation for that function. Where is the missing documentation?

Also, if the user has already imported a VCF file into R using readVcf from VariantAnnotation and done some subsetting to it, could writing a temporary file to disk and re-importing it into R be avoided by being able to work directly with the VCF objects?

> somatics
class: CollapsedVCF 
dim: 31 2 
rowRanges(vcf):
  GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
  DataFrame with 23 columns: CONTQ, DP, ECNT, GERMQ, MBQ, MFRL, MMQ, MPOS, NALOD, NCount, NLOD...