Homologous recombination deficiency signatures from cancer copy number alteration profiles from SNP-arrays

Submission contains R script for calculation of three signatures of Homologous Recombination Deficiency (HRD) based on absolute copy number alteration profile obtained from SNP arrays. An example txt file with copy number alteration profile is also provided. Three signatures include: HRD_LOH {Abkevich et al, 2012, Br.J.Cancer}, NTAI {Birkbak et al, 2012, Cancer Discovery} and LST {Popova et al, 2012, Cancer Research}. 

This script was used to obtain HRD signatures for the SNP array data used in the article Petra ter Brugge et al, "Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers", Nat.Commun. 2022.