This R package contains various functions to produce input data for DPClust using SNV variant calls and copy number data from Battenberg. Most importantly, it contains the runGetDirichletProcessInfo function that produces the input data for SNV based clustering.

dpclust3p is an R package and can be installed with the commands right below. It also requires the alleleCounter tool to be in $PATH.

source("http://bioconductor.org/biocLite.R"); biocLite(c("optparse","VariantAnnotation","GenomicRanges","Rsamtools","ggplot2","IRanges","S4Vectors","reshape2"))'
devtools::install_github("Wedge-Oxford/dpclust3p")

The typical usage is to create the DPClust input data. See inst/example for a few example pipelines. A pipeline typically consists of three steps:

• Transform loci from a VCF file into a loci file
• Obtain allele counts for all mutations, either by invoking alleleCount or by dumping counts from the VCF file
• Convert allele counts and copy number information into DPClust input

The R package contains many functions from which one can build their own pipeline

This package has been Dockerised, build as follows:

docker build -t dpclust3p:1.0.8 .