reduceArms: Reduce Arm/Seg level CN to an aneuploidy score

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

Description

Takes the Arm and Seg level CN classification (Loss (-1), Neut (0), Gain(1)) from the getCAA() function and reduces this data into a single matrix of chromosomal-arm level value (e.g. chr1p: 1)

Usage

reduceArms(
  segf_caa,
  caa_method = c("arm", "seg"),
  threshold = NA,
  arm_ids = c("p", "q"),
  verbose = FALSE
)

Arguments

segf_caa	Output from getCAA(), GRanges of individual chromosomes [GRangesList]
caa_method	The chromosomal-arm aneuploidy scoring metric to use: [Vector] - 'arm': Reduces the arm-level CN classifications (classified from the Weighted Median of the chr-arm CN) to a single value - 'seg': Uses a threshold (or weighted median if no threshold given) on the chr-arm CN classifications across all arm-level segs
threshold	For 'seg' caa_method, how much of a chr-arm must be gained or lost to get -1 or 1 score
arm_ids	[Default c("p", "q")]
verbose	verbose statement

Value

A matrix of aneuploidy scores [chr-arms x caa_methods]

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