| snpgdsGDS2PED {SNPRelate} | R Documentation |
Convert a GDS file to a PLINK ped file.
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 ( |
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 |
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/
# open an example dataset (HapMap) genofile <- snpgdsOpen(snpgdsExampleFileName()) # GDS ==> PED snpgdsGDS2PED(genofile, ped.fn="tmp") # close the GDS file snpgdsClose(genofile)