haps-format: SHAPEIT haps/sample format

In stefanedwards/Siccuracy: Pipeline Package for AlphaImpute

Description

read.haps loads SHAPEIT haps/sample into a haps object.

haps class requires a list object with three elements, haps, sample, and map, with corresponding dimensions.

write.haps writes haps object to haps/sample file formats

Usage

read.haps(haps, sample = NULL)

is.haps(x)

as.haps(x)

write.haps(x, haps, sample)

Arguments

haps	Filename of .haps file.
sample	Filename of .sample file. If NULL (default), uses filestem of haps appended with .sample.
x	Object to test or convert

Details

read.haps accepts compressed files (.gz and .bz2, see connections), but then both filename arguments must be given.

is.haps doesn't actually test if x inherits from class haps, just that the contents matches.

Value

read.haps returns a list with three entries:

samples:

Data fram with contents of .sample file (three columns).

haps:

Matrix with unphased genotypes of each allele, with each loci per row and indivduals in tuples of columns.

map:

Data frame with map of loci, i.e. chromosome, snp ID, chromosomal position, and the two alleles.

See Also

extract.gt for vcfR-style extraction of genotypes

stefanedwards/Siccuracy documentation built on May 30, 2019, 10:44 a.m.