ascatToHRDLOH: HRD-LOH index from ASCAT

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

HRD-LOH index from ASCAT

Description

Compute the HRD-LOH index starting from a data fram (possibly loaded from an ASCAT output file) with the following columns: 'seg_no', 'Chromosome', 'chromStart', 'chromEnd', 'total.copy.number.inNormal', 'minor.copy.number.inNormal', 'total.copy.number.inTumour', 'minor.copy.number.inTumour'

Usage

ascatToHRDLOH(ascat.data, SAMPLE.ID, return.loc = FALSE)

Arguments

ascat.data	data frame with the following columns: 'seg_no', 'Chromosome', 'chromStart', 'chromEnd', 'total.copy.number.inNormal', 'minor.copy.number.inNormal', 'total.copy.number.inTumour', 'minor.copy.number.inTumour'
SAMPLE.ID	sample name
return.loc	if TRUE return the HRD-LOH regions, while if FALSE return the HRD-LOH index (i.e. the count of the regions) instead.

Value

returns the HRD-LOH index or regions

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

ascat.data <- read.table("ascat.scv",sep=",",header=TRUE)
hrd_index <- ascatToHRDLOH(ascat.df,"test_sample")

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