snpgdsGDS2BED: Conversion from GDS to PLINK BED

In zhengxwen/SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Conversion from GDS to PLINK BED

Description

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

Usage

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

Arguments

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

Details

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.

Value

None.

Author(s)

Xiuwen Zheng

References

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/

See Also

snpgdsBED2GDS, snpgdsGDS2PED

Examples

# 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)

zhengxwen/SNPRelate documentation built on Nov. 19, 2024, 1:02 p.m.