ascatToHRDLOH: HRD-LOH index from ASCAT

In pdiakumis/hrdetect: Signature Tools

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)

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

Value

returns the HRD-LOH index

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")

pdiakumis/hrdetect documentation built on May 17, 2020, 5:30 p.m.