snpgdsGDS2PED: Conversion from GDS to PED
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 ped file.

1 2	snpgdsGDS2PED(gdsobj, ped.fn, sample.id=NULL, snp.id=NULL, use.snp.rsid=TRUE, format=c("A/G/C/T", "A/B", "1/2"), verbose=TRUE)

`gdsobj`	a GDS file object (`gds.class`)
`ped.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
`use.snp.rsid`	if `TRUE`, use "snp.rs.id" instead of "snp.id" if available
`format`	specify the coding: "A/G/C/T" – allelic codes stored in "snp.allele" of the GDS file; "A/B" – A and B codes; "1/2" – 1 and 2 codes
`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.

PED – the PLINK text 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/

snpgdsGDS2BED

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

snpset <- snpgdsSelectSNP(genofile, missing.rate=0.95)
snpgdsGDS2PED(genofile, ped.fn="tmp", snp.id=snpset)

# close the genotype file
closefn.gds(genofile)