write.mach: Write a snpStats object in mach format

In snpStatsWriter: Flexible writing of snpStats objects to flat files

Description

see write.simple for general information

Usage

  write.mach(X, a1, a2, pedfile, mfile,
    pedigree = rownames(X), member = rep(1, nrow(X)),
    father = rep(0, nrow(X)), mother = rep(0, nrow(X)),
    sex = rep("M", nrow(X)), snp.names = colnames(X))

Arguments

pedfile	Output pedigree file name.
mfile	Output marker file name.
pedigree	Optional pedigree/member/father/mother/sex indentifier vectors, same order as rows in snpStats object. If missing, pedigree is set to rownames(X) and the others default to unrelated males
member	See pedigree
father	See pedigree
mother	See pedigree
sex	See pedigree
snp.names	optional SNP names to include in the marker map file. Defaults to colnames(X).
X	SnpMatrix object
a1	vector of first allele at each SNP
a2	vector of second allele at 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]
pf <- tempfile()
mf <- tempfile()

## write in suitable format for MACH
nsnps <- ncol(A.small)
write.mach(A.small, a1=rep("1",nsnps), a2=rep("2",nsnps), pedfile=pf, mfile=mf)
unlink(pf)
unlink(mf)

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