snpgdsGDS2BED: Conversion from GDS to PLINK BED
In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

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

Convert a GDS file to a PLINK binary ped (BED) file.

1 2	snpgdsGDS2BED(gdsobj, bed.fn, sample.id=NULL, snp.id=NULL, snpfirstdim=NULL, verbose=TRUE)

`gdsobj`	an object of class `SNPGDSFileClass`, a SNP GDS file; or characters, the file name of GDS
`bed.fn`	the file name of output, without the filename extension ".bed"
`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
`snpfirstdim`	if TRUE, genotypes are stored in the individual-major mode, (i.e, list all SNPs for the first individual, and then list all SNPs for the second individual, etc); if NULL, determine automatically
`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 <- snpgdsOpen(snpgdsExampleFileName())

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

# close the genotype file
snpgdsClose(genofile)


# delete the temporary files
unlink(c("test.bed", "test.bim", "test.fam"), force=TRUE)