rel2abs: rel2abs

In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

rel2abs

Description

rescales CN values from relative to "absolute" (i.e. per cancer cell copy) scale given purity and ploidy

Usage

rel2abs(
  gr,
  purity = NA,
  ploidy = NA,
  gamma = NA,
  beta = NA,
  field = "ratio",
  field.ncn = "ncn"
)

Arguments

gr	GRanges input with meta data field corresponding to mean relative copy "mean" in that interval
purity	purity of sample
ploidy	ploidy of sample
gamma	gamma fit of solution (over-rides purity and ploidy)
beta	beta fit of solution (over-rides purity and ploidy)
field	meta data field in "gr" variable from which to extract signal, default "mean"
field.ncn	meta data field in "gr" variable from which to extract germline integer copy number, default "ncn", if doesn't exist, germline copy number is assumed to be zero

Details

takes in gr with signal field "field"

Value

numeric vector of integer copy numbers

mskilab/gGnome documentation built on May 8, 2024, 4:25 p.m.