calc.hrd: HRD-LOH index

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

HRD-LOH index

Description

This function is an implementation of the cisplatin predictor developed by Myriad with Gordon Mills PMID: 23047548. Abkevichs cutoffs: > 10, found in the supplementary info.

Usage

calc.hrd(seg, nA = 7, check.names = FALSE, return.loc = FALSE)

Arguments

seg	seg must be an ASCAT output object, in DNAcopy format. Requires the following columns in the given order: "SampleID", "Chromosome", "Start", "End", "nProbes", "totalCN", "nA", "nB", "Ploidy" and "AberrantCellFraction". Column "nProbes", "Ploidy" and "AberrantCellFraction" are not used here and can be set to NA.
nA	is the column where copy number of A allele is found. This needs to be set to 7, because of the columns are referenced by position according to the required column order of seg.

Author(s)

Nicolai Juul Birkbak, [e-mail]

References

Abkevich, V., Timms, K. M., Hennessy, B. T., Potter, J., Carey, M. S., Meyer, L. a., ... Lanchbury, J. S. (2012). Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer. British Journal of Cancer, 107(10), 1776–82. https://doi.org/10.1038/bjc.2012.451

Examples

HRD_LOH <- calc.hrd(ascat.data2, nA=7,check.names=FALSE, return.loc=FALSE)

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.