checkIfWGD: Whole genome doubling checker

In quevedor2/aneuploidy_score: Calculate the Aneuploidy Score from Chromosome Arm SCNAs/Aneuploidies

Description

Takes a .seg file data frame and estimates whether the tumor is whole-genome doubled (WGD). This function requries Total Copy Number and will not work using L2R.

Usage

checkIfWGD(
  segf,
  tcn_col,
  threshold = 0.5,
  input_ploidy = NA,
  wgd_gf = 0.5,
  ploidy_method = "wmean"
)

Arguments

segf	.Seg Data [Data frame]
tcn_col	Column ID for CN value [String]
threshold	The threshold to call a gain or loss relative to base ploidy (ploidy +/- threshold) (Default: 0.5) [Numeric]
input_ploidy	If you want to use a specific ploidy-value
wgd_gf	Genomic fraction above base_ploidy + threshold to be considered genome doubled (Default: 0.5) [Numeric]
ploidy_method	Calculates the base ploidy [Character] - 'wmean': Segment size weighted CN mean - 'wmedian': Segment size weighted CN median - 'mean': CN mean - 'median': CN median - 'multi_base2': Nearest base ploidy 2 (e.g. CN=3 -> ploidy of 4) - 'input': Use a specified ploidy value

Value

A named vector ploidy: Ploidy as estimated by ploidy_method WGD: Boolean indicated whether sample is WGD

quevedor2/aneuploidy_score documentation built on Feb. 26, 2021, 12:13 p.m.