| snpgdsGDS2Eigen {SNPRelate} | R Documentation |
Convert a GDS file to an EIGENSTRAT file.
snpgdsGDS2Eigen(gdsobj, eigen.fn, sample.id=NULL, snp.id=NULL, verbose=TRUE)
gdsobj |
an object of class |
eigen.fn |
the file name of EIGENSTRAT |
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 |
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.
Eigen – the text format used in EIGENSTRAT.
None.
Xiuwen Zheng
Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genetics 2:e190.
Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 38, 904-909.
http://corearray.sourceforge.net/
# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())
snpset <- snpgdsSelectSNP(genofile, missing.rate=0.95)
snpgdsGDS2Eigen(genofile, eigen.fn="tmpeigen", snp.id=snpset)
# close the genotype file
snpgdsClose(genofile)
# delete the temporary files
unlink(c("tmpeigen.eigenstratgeno", "tmpeigen.ind", "tmpeigen.snp"), force=TRUE)