get_gene_ampdels_from_jabba: get_gene_ampdels_from_jabba

In mskilab/skitools: Various mskilab R utilties

get_gene_ampdels_from_jabba

Description

Takes a jabba_rds output and returns a GRanges with the genes that have either amplifications or deletions

Usage

get_gene_ampdels_from_jabba(
  jab,
  pge,
  amp.thresh = 4,
  del.thresh = 0.5,
  nseg = NULL
)

Arguments

jab	either path to jabba_rds output or an object containing the jabba output
pge	GRanges of genes (must contain field "gene_name")
amp.thresh	threshold to determine amplifications (this is relative to the ploidy normalized copy number. Values are also normalized using the normal copy number so that amplifications and deletions in chromosome X in male samples can be called correctly.
del.thresh	threshold to determine deletions.
nseg	GRanges with field "ncn" - the normal copy number (if not provided then ncn = 2 is used)

Value

scna data.table with genes that have either amplification or deletion

Author(s)

Alon Shaiber

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.