scar_score: Scar score

In farkkilab/scarHRD: Estimating Genomic scars signatures (LST, TAI,LOH)

Description

Determining genomic scar score (telomeric allelic imbalance, loss-off heterozigosity, large-scle transitions), signs of homologous recombination deficiency

Usage

scar_score(seg, reference = "grch38", seqz = FALSE, ploidy = NULL,
  sizelimitLOH = 1.5e+07, outputdir = NULL)

Arguments

seg	Imput file: either a binned sequenza out file (or any other segmentation file with the following columns: chromosome, position, base.ref, depth.normal, depth.tumor, depth.ratio, Af, Bf, zygosity.normal, GC.percent, good.reads, AB.normal, AB.tumor, tumor.strand) or an allele-specific segmentation file with the following columns: 1st column: sample name, 2nd column: chromosome, 3rd column: segmentation start, 4th column: segmentation end, 5th column: total copynumber, 6th column: copy number of A allele, 7th column: copy number of B allele
seqz	Optional parameter, set to TRUE, if input file is a binned sequenza file.
ploidy	Optional parameter, may be used if the ploidy of the sample is known.
reference:	reference genome: either grch38 or grch37. Default is grch38.

Value

Output is, with the following columns: HRD Telomeric AI Mean size Interstitial AI Mean Size Whole chr AI Telomeric LOH Mean size Interstitial LOH Mean Size Whole chr LOH Ploidy Aberrant cell fraction LST HRDscore adjustedHRDscore

farkkilab/scarHRD documentation built on May 6, 2020, 6:32 p.m.