write.beagle: Write a snpStats object in beagle format

In snpStatsWriter: Flexible writing of snpStats objects to flat files

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.

Author(s)

Chris Wallace

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)

snpStatsWriter documentation built on May 2, 2019, 5:41 a.m.