snpgdsGDS2Eigen: Conversion from GDS to Eigen (EIGENSTRAT)

In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Description

Convert a GDS file to an EIGENSTRAT file.

Usage

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

Arguments

gdsobj	an object of class SNPGDSFileClass, a SNP GDS file
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

Details

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.

Value

None.

Author(s)

Xiuwen Zheng

References

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/

See Also

snpgdsGDS2PED

Examples

# 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)

SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.