getHRD.Score: get the standard HRD score

In jpluta26/HRDX:

Description

get the standard HRD score

Usage

getHRD.Score(seq.dat, CN.dat, min.seg.size = 1.1e+07,
  scaleTotal = FALSE, type = "sum")

Arguments

seq.dat	the preprocessed sequencing data
CN.dat	the copy number data
min.seg.size	optional: the minimum segment size (default to 11Mbp)
scaleTotal	optional: rescale the total to range of 0-100
type	optional: type of score to return, one of "sum" or "average"
ploidy.dat	the ploidy data

Details

calculates the 'standard' HRD score: the sum of LST, LOH, and NTAI, all normalized. Can optionally return the HRD score rescaled to a range of 0 - 100.

Value

a numeric value representing the HRD score

Examples

seq.dat <- preprocessHRD( sub01.segments )

CN.dat <- getCNT( seq.dat )
HRD <- getHRD.Score( seq.dat, CN.dat, sub01.ploidy, scaleTotal = FALSE)

jpluta26/HRDX documentation built on Nov. 10, 2019, 10:41 p.m.