| snpgdsGDS2BED {SNPRelate} | R Documentation |
Convert a GDS file to a PLINK binary ped file.
snpgdsGDS2BED(gdsobj, bed.fn, sample.id=NULL, snp.id=NULL, snpfirstdim=NULL,
verbose=TRUE)
gdsobj |
an object of 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 |
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/
# 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)