README.md

In eyzhao/hrdtools: Homologous Recombination Deficiency Tests with Whole Genome Sequencing

HRDtools

HRDtools is an R package which computes HRD scores and mutation signatures in individual tumours.

Citation

If you use HRDtools in your publication, please cite the following study:

Zhao EY, Shen Y, Pleasance E, ... Jones SJM, Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer. Clinical Cancer Research. 2017 Dec 15;23(24):7521-7530

Installation

HRDtools is an R package, and can be installed via devtools.

devtools::install_github('eyzhao/hrdtools')

HRDtools has numerous package dependencies, which may need to be installed first.

install.packages(c(
  'tidyverse',
  'nnls',
  'parallel',
  'snow',
  'snowfall',
  'plyr'
))

source("https://bioconductor.org/biocLite.R")
bioclite(c(
  'GenomicRanges',
  'VariantAnnotation',
  'SomaticSignatures',
  'BSgenome'
))

Usage

Once installed, HRDtools can be used in R as follows,

library(hrdtools)

run_test(
  'path/to/segments.file.tsv'
)

where the file path/to/segments.file.tsv contains CNV/LOH segments. HRDtools was tested on output from APOLLOH, but in theory any CNV caller with LOH support should work, so long as the LOH calling state names are modified to match those given by APOLLOH.

The segments file should contain one segment per row, with the columns chr, start, end, copynumber, lohtype. If different column names are used to denote copy number and LOH, they can be specified as follows.

run_test(
  'path/to/segments.file.tsv',
  loh.col = 'loh_state',
  cnv.col = 'tumour_copy_number'
)

eyzhao/hrdtools documentation built on May 21, 2019, 3:09 a.m.