oxford: Oxford format

Description Usage Arguments Value

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

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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.