copy_number_scores: Copy-number based scores

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

Copy-number based scores

Description

Calculate the following

Fraction of genome altered:

Fraction of genome altered and genome doubling flag.

Fraction LOH:

Fraction of genome with LOH and flag for hypoploidy.

LST score:

Large-scale state transitions, see source URL.

NtAI:

Telomeric allelic imbalance, see source URL.

HRD-LOH:

HRD-LOH score, see source URL.

Usage

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

calculate_loh(segs, snps, genome = c("hg19", "hg18", "hg38"),
  algorithm = c("em", "cncf"), hypoploidy_threshold = 0.5)

calculate_ntai(segs, ploidy, genome = c("hg19", "hg18", "hg38"),
  algorithm = c("em", "cncf"), min_size = 0, min_probes = 250)

calculate_lst(segs, ploidy, genome = c("hg19", "hg18", "hg38"),
  algorithm = c("em", "cncf"), min_size = 1e+07, min_probes = 50)

calculate_hrdloh(segs, ploidy, algorithm = c("em", "cncf"))

Arguments

segs	FACETS segmentation output.
ploidy	Sample ploidy.
genome	Genome build.
algorithm	Choice between FACETS em and cncf algorithm.
snps	FACETS SNP output.
hypoploidy_threshold	Threshold for hypoploid call.
min_size	Minimum length of segment, as defined per function.
min_probes	Minimum number of SNPs per segment, as defined per function.

Value

List with one or more values from function.

Source

https://www.ncbi.nlm.nih.gov/pubmed/26015868

Examples

calculate_fraction_cna(test_facets_output$segs, test_facets_output$ploidy, 'hg38', 'em')
calculate_loh(test_facets_output$segs, test_facets_output$snps, 'hg38', 'em')
calculate_lst(test_facets_output$segs, test_facets_output$ploidy, 'hg38', 'em')
calculate_ntai(test_facets_output$segs, test_facets_output$ploidy, 'hg38', 'em')
calculate_hrdloh(test_facets_output$segs, test_facets_output$ploidy, 'em')

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