This R package contains various functions to produce input data for DPClust using SNV variant calls and segment copy number data from [ASCAT]. 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 below. It also requires the alleleCounter tool to be in $PATH, when run locally.
source("http://bioconductor.org/biocLite.R"); biocLite(c("optparse","VariantAnnotation","GenomicRanges","Rsamtools","ggplot2","IRanges","S4Vectors","reshape2"))'
devtools::install_github("OpenGenomics/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
| File | Description |
|---|---|
| preprocessing.R | Main preprocessing functions to create DPClust input, perform mutation phasing, filter by mutational signature |
| allelecount.R | Functions to count alleles in a BAM file, or dump counts from a range of VCF formats |
| kataegis.R | Functions to identify kataegis events (requires fastPCF.R) |
| copynumber.R | Various functions related to copy number |
| qualitycontrol.R | Create plots that can be used for QCing |
| interconvertMutationBurdens.R | Basic functions for data transformations |
| util.R | Various utility functions |
This package has been Dockerised, build as follows:
docker build -t quay.io/ohsugdanpipelines/dpclust3p .