granges-utils: GRanges converter functions

In comm03/trysomesigs: Somatic Signatures

Description

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

Usage

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

Arguments

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

Details

• 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.

Value

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

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

See Also

seqnames, mcols

seqlevelsStyle

Examples

  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)
  

comm03/trysomesigs documentation built on May 15, 2019, 1:14 p.m.