snpStatsWriter (version 1.5-6)

write.beagle: Write a snpStats object in beagle format

Description

see write.simple for general information

Usage

write.beagle(X, a1, a2, bp, trait = NULL, gfile, mfile)

Arguments

trait

disease trait (0=missing, 1=control, 2=case)

gfile,mfile

gfile=genotype file, pedfile=pedigree file

X

SnpMatrix object

a1

vector of first allele at each SNP

a2

vector of second allele at each SNP

bp

vector of base pair positions for each SNP

Value

No return value, but has the side effect of writing specified output files.

Examples

data(testdata,package="snpStats")
A.small <- Autosomes[1:6,1:10]
gf <- tempfile()
mf <- tempfile()

## write in suitable format for beagle
nsnps <- ncol(A.small)
write.beagle(A.small, a1=rep("1",nsnps), a2=rep("2",nsnps), bp=1:nsnps, gfile=gf, mfile=mf)
unlink(gf)
unlink(mf)