snpgdsGDS2Eigen: Conversion from GDS to Eigen (EIGENSTRAT)
In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

Description Usage Arguments Details Value Author(s) References See Also Examples

Convert a GDS file to an EIGENSTRAT file.

1	snpgdsGDS2Eigen(gdsobj, eigen.fn, sample.id=NULL, snp.id=NULL, verbose=TRUE)

`gdsobj`	a GDS file object (`gds.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/

snpgdsGDS2PED

# open an example dataset (HapMap)
genofile <- openfn.gds(snpgdsExampleFileName())

snpset <- snpgdsSelectSNP(genofile, missing.rate=0.95)
snpgdsGDS2Eigen(genofile, eigen.fn="tmpeigen", snp.id=snpset)

# close the genotype file
closefn.gds(genofile)