getCAA: Seg to CN Chromosomal Fractions

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

Description

Takes a .seg data-frame and finds out for each CN interval, what fraction of the chromosomal arm or chromosome does it occupy. It calculates this metric across all covered regions in (NA- excluded) or the entire chromosomal-arm/chromosome (NA-included). It also supports the Shukla et al. method of removing segments that overlap the centromere.

Usage

getCAA(
  segf,
  cytoarm,
  tcn_col,
  filter_centromere = FALSE,
  classifyCN = FALSE,
  ploidy = 0,
  threshold = 0.2,
  ...
)

Arguments

segf	.Seg Data [Data frame]
cytoarm	Output of cytobandToArm() function [List of Data frames]
tcn_col	Column ID for CN value [String]
filter_centromere	Whether to include or exclude segments
classifyCN	classify arm-CN into Loss/Neut/Gain [Boolean]
ploidy	base-ploidy for Loss/Neut/Gain estimation [Default=0]
threshold	Threshold around ploidy (+/- threshold) [Default=0.2]
...	Parameters for .classifyCN() function (ploidy, threshold, verbose)

Value

A GRangesList split by chromosome with each interval representing a reduced chromosomal aberration and its associated chromosomal_arm and chromosome fraction with and without NAs factored in

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