writeInputsFastphase: Write inputs for fastPHASE

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Write inputs for fastPHASE

Description

Use the external software fcGENE from Roshyara and Scholz (2014).

Usage

writeInputsFastphase(X, snp.coords, alleles, file, verbose = 0)

Arguments

X	matrix of bi-allelic SNP genotypes encoded, for each SNP, in number of copies of its second allele, i.e. as allele doses in 0,1,2, with genotypes in rows and SNPs in columns; the "second" allele is arbitrary, it corresponds to the second column of alleles, which can be the minor or the major allele
snp.coords	data.frame with SNP identifiers as row names, and two columns, "chr" and "coord" or "pos"
alleles	data.frame with SNPs in rows (names as row names) and alleles in columns (exactly 2 columns are required); the second column should correspond to the allele which number of copies is counted at each SNP in X
file	write the genotype data to this file (for instance 'genotypes_fastphase.txt' or 'genotypes_fastphase.txt.gz', but don't use gzfile)
verbose	verbosity level (0/1/2)

Value

nothing

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.