snpgdsGDS2BED: Conversion from GDS to PLINK BED
In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

Description Usage Arguments Details Value Author(s) References See Also Examples

Convert a GDS file to a PLINK binary ped file.

1	snpgdsGDS2BED(gdsobj, bed.fn, sample.id=NULL, snp.id=NULL, verbose=TRUE)

`gdsobj`	a GDS file object (`gds.class`)
`bed.fn`	the file name of output
`sample.id`	a vector of sample id specifying selected samples; if NULL, all samples are used
`snp.id`	a vector of snp id specifying selected SNPs; if NULL, all SNPs are used
`verbose`	if TRUE, show information

GDS – Genomic Data Structures, the extended file name used for storing genetic data, and the file format used in the gdsfmt package.

BED – the PLINK binary ped format.

None.

Xiuwen Zheng

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.

http://corearray.sourceforge.net/

snpgdsBED2GDS, snpgdsGDS2PED

# open an example dataset (HapMap)
genofile <- openfn.gds(snpgdsExampleFileName())

snpset <- snpgdsSelectSNP(genofile, missing.rate=0.95)
snpgdsGDS2BED(genofile, bed.fn="test", snp.id=snpset)

# close the genotype file
closefn.gds(genofile)