oxford: Oxford format

In stefanedwards/Siccuracy: Pipeline Package for AlphaImpute

Description

Oxford format is a flat, single file, with a single loci per row. The columns are chromosome, SNP ID, (chromosomal) position, reference allele and alternative allele. Following triplets of columns denote each sample's genotype dosage / probability.

Usage

read.oxford(file, ...)

is.oxford(x)

write.oxford(x, file, ...)

Arguments

file	Filename to read from or write to.
...	Parameters forwarded to read.table or write.table,
x	Oxford object.

Value

read.oxford returns an oxford object, i.e. a list with two entries:

map:

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

probs:

3 dimensional array; rows (d1) are loci, columns (d2) are samples, in three layers comprising gene dosage of homozygote for reference allele, heterozygote, and homozygote for alternative allele.

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