write.impute: Write a snpStats object in IMPUTE format

In chr1swallace/snpStatsWriter: Flexible Writing of snpStats Objects to Flat Files

Description

see write.simple for general information

Usage

write.impute(X, a1, a2, bp, fileroot, rs.id = NULL, snp.id = NULL)

Arguments

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
fileroot	Root of output file names. fileroot.gen and fileroot.sample will be created.
rs.id	vector of rs ids (if empty, will set to rownames(X))
snp.id	vector of snp ids (if empty, will set to S1...Sn)

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]
pf <- tempfile()

## write in suitable format for IMPUTE
nsnps <- ncol(A.small)
write.impute(A.small, a1=rep("1",nsnps), a2=rep("2",nsnps), bp=1:nsnps, fileroot=pf)
unlink(pf)

chr1swallace/snpStatsWriter documentation built on May 13, 2019, 6:20 p.m.