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
Value
None.
Details
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.
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.
# open an example dataset (HapMap)genofile <- snpgdsOpen(snpgdsExampleFileName())
# GDS ==> PEDsnpgdsGDS2PED(genofile, ped.fn="tmp")
# close the GDS filesnpgdsClose(genofile)