getBAFsAndLogRs: Obtain BAF and LogR from the allele counts
In Wedge-Oxford/battenberg: Battenberg subclonal copy number caller

getBAFsAndLogRs

R Documentation

Obtain BAF and LogR from the allele counts

Description

Obtain BAF and LogR from the allele counts

Usage

getBAFsAndLogRs(
  tumourAlleleCountsFile.prefix,
  normalAlleleCountsFile.prefix,
  figuresFile.prefix,
  BAFnormalFile,
  BAFmutantFile,
  logRnormalFile,
  logRmutantFile,
  combinedAlleleCountsFile,
  chr_names,
  g1000file.prefix,
  minCounts = NA,
  samplename = "sample1",
  seed = as.integer(Sys.time())
)

Arguments

`tumourAlleleCountsFile.prefix`	Prefix of the allele counts files for the tumour.
`normalAlleleCountsFile.prefix`	Prefix of the allele counts files for the normal.
`figuresFile.prefix`	Prefix for output figures file names.
`BAFnormalFile`	File where BAF from the normal will be written.
`BAFmutantFile`	File where BAF from the tumour will be written.
`logRnormalFile`	File where LogR from the normal will be written.
`logRmutantFile`	File where LogR from the tumour will be written.
`combinedAlleleCountsFile`	File where combined allele counts for tumour and normal will be written.
`chr_names`	A vector with allowed chromosome names.
`g1000file.prefix`	Prefix to where 1000 Genomes reference files can be found.
`minCounts`	Integer, minimum depth required for a SNP to be included (optional, default=NA).
`samplename`	String, name of the sample (optional, default=sample1).
`seed`	A seed to be set for when randomising the alleles.