snpgdsGDS2Eigen {SNPRelate} | R Documentation

## Conversion from GDS to Eigen (EIGENSTRAT)

### 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)

[Package SNPRelate version 1.18.1 Index]