granges-utils: GRanges converter functions
In julian-gehring/SomaticSignatures: Somatic Signatures

Description Usage Arguments Details Value See Also Examples

A set of utilities functions to convert and extract data in 'GRanges' objects.

1
2
3

  ncbi(x)
  ucsc(x)
  seqchar(x)

`x`	A 'GRanges' object or one inheriting from the 'GRanges' class [required].

grangesExtracts only the 'GRanges' information by dropping the metadata columns of the object. The 'seqinfo' slot is kept.
ncbi, ucscShorthand for converting the seqnames notation to 'UCSC' (e.g. 'chr1', 'chrM') or 'NCBI' (e.g. '1', 'MT”) notation, respectively. This also sets the 'genome' slot in the 'seqinfo' field to 'NA'.
seqcharExtracts the 'seqnames' as a character vector.

For 'ncbi', 'ucsc': An object of the same class as the input.

For 'seqchar': A character vector with 'seqnames'.

seqnames, mcols

seqlevelsStyle

  mutect_path = system.file("examples", "mutect.tsv", package = "SomaticSignatures")
  vr1 = readMutect(mutect_path, strip = TRUE)
  
  ## extract the GRanges
  gr = granges(vr1)
  
  ## convert back and forth
  gr_ncbi = ncbi(gr)
  gr_ucsc = ucsc(gr_ncbi)
  
  identical(gr, gr_ucsc)
  
  ## extract the seqnames as a character vector
  seq_chars = seqchar(gr)