preProcessGeneCnv: Subsets PURPLE gene cnv file for genes of interest

In luannnguyen/hmfGeneAnnotation: Determines gene amplifications and biallelic losses from HMF pipeline output

Description

Subsets PURPLE gene cnv file for genes of interest

Usage

preProcessGeneCnv(
  gene.cnv.file,
  out.file,
  bed.file = BED_FILE,
  genes.enst2ensg.file = GENES_ENST2ENSG,
  verbose = T
)

Arguments

gene.cnv.file	Path to PURPLE gene cnv file
out.file	Path to output file
bed.file	Path to bed file specifying the genome intervals to keep (defaults ot the one stored in this package)
genes.enst2ensg.file	Path to lookup table to convert ENSEMBL transcript to genes ids
verbose	Show progress messages?

Value

Nothing but writes the subsetted PURPLE gene cnv txt file

luannnguyen/hmfGeneAnnotation documentation built on May 6, 2020, 1:07 p.m.