HRDtools is an R package which computes HRD scores and mutation signatures in individual tumours.
If you use HRDtools in your publication, please cite the following study:
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'
))
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'
)
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