arm_level_changes: Arm-level changes

In mskcc/facets-suite: Functions to run and parse output from FACETS

Arm-level changes

Description

Get the altered chromosome arms in sample. Does not include the acrocentric p arms of chromosomes 12, 14, 15, 31, and 22.

Usage

arm_level_changes(segs, ploidy, genome = c("hg19", "hg18", "hg38"),
  algorithm = c("em", "cncf"))

Arguments

segs	FACETS segmentation output.
ploidy	Sample ploidy.
genome	Genome build.
algorithm	Choice between FACETS em and cncf algorithm.

Value

List of items, containing:

data.frame for all genes mapping onto a segment in the output segmentation, with the columns:

• genome_doubled: Boolean indicating whether sample genome is doubled.

• fraction_cna: Fraction of genome altered.

• weighted_fraction_cna: A weighted version of fraction_cna where only altered chromosomes are counted and weighted according to their length relative to total genome.

• aneuploidy_scores: Count of the number of altered arms, see source URL.

• full_output: Full per-arm copy-number status.

Source

https://www.ncbi.nlm.nih.gov/pubmed/29622463

mskcc/facets-suite documentation built on Sept. 13, 2022, 4:14 a.m.