generate.impute.input.wgs: Prepare data for impute
In Wedge-lab/battenberg: Battenberg subclonal copy number caller

generate.impute.input.wgs

R Documentation

Prepare data for impute

Description

Prepare data for impute

Usage

generate.impute.input.wgs(
  chrom,
  tumour.allele.counts.file,
  normal.allele.counts.file,
  output.file,
  imputeinfofile,
  is.male,
  problemLociFile = NA,
  useLociFile = NA,
  heterozygousFilter = 0.1
)

Arguments

`chrom`	The chromosome for which impute input should be generated.
`tumour.allele.counts.file`	Output from the allele counter on the matched tumour for this chromosome.
`normal.allele.counts.file`	Output from the allele counter on the matched normal for this chromosome.
`output.file`	File where the impute input for this chromosome will be written.
`imputeinfofile`	Info file with impute reference information.
`is.male`	Boolean denoting whether this sample is male (TRUE), or female (FALSE).
`problemLociFile`	A file containing genomic locations that must be discarded (optional).
`useLociFile`	A file containing genomic locations that must be included (optional).
`heterozygousFilter`	The cutoff where a SNP will be considered as heterozygous (default 0.01).