parse.imputeinfofile: Read in the imputeinfofile.
In Wedge-Oxford/battenberg: Battenberg subclonal copy number caller

parse.imputeinfofile

R Documentation

Read in the imputeinfofile.

Description

Reads in a file with the following columns: chromosome : 1-X impute_legend : Legend file in IMPUTE -l format genetic_map : Genetic map file in IMPUTE -m format impute_hap : Phased haplotype file in IMPUTE -h format start : Start of the chromosome end : End of the chromosome is_par : 1 when pseudo autosomal region, 0 when not

Usage

parse.imputeinfofile(imputeinfofile, is.male, chrom = NA)

Arguments

`imputeinfofile`	Path to the imputeinfofile on disk.
`is.male`	A boolean describing whether the sample under study is male.
`chrom`	The name of a chromosome to subset the contents of the imputeinfofile with (optional)