facets_jointsegs_parse_to_gr: Parse jointsegs into GRanges object

In brucemoran/somenone: R functions required by the somenone NextFlow nf-core pipeline

Parse jointsegs into GRanges object

Description

Parse jointsegs into GRanges object

Usage

facets_jointsegs_parse_to_gr(
  jointseg,
  sampleID,
  which_genome,
  anno = NULL,
  cgc_gr = NULL,
  bsgenome = NULL,
  work_dir
)

Arguments

jointseg	filename (output from Facets) with columns: "seg", "num.mark", "nhet", "cnlr.median", "mafR", "segclust", "cnlr.median.clust", "mafR.clust", "cf.em", "tcn.em", "lcn.em"
sampleID	the sample identifier, taken as the string before first dot in jointseg
which_genome	the genome assembly used, "hg19" or "hg38"
anno	annotation strategy, "ENS" or "CGC"
cgc_gr	GRanges object of cancer gene census from COSMIC
bsgenome	which version of bsgenome to use
work_dir	character path of where files should be found, written (default: ./)

Value

a GRanges object with annotated jointsegs from input

brucemoran/somenone documentation built on Nov. 1, 2022, 3:56 p.m.