snpgdsGDS2PED {SNPRelate} | R Documentation

## Conversion from GDS to PED

### Description

Convert a GDS file to a PLINK text ped file.

### Usage

    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)

### Arguments

`gdsobj` | a GDS file object (`gds.class`)
`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 `TRUE`, use "snp.rs.id" instead of "snp.id" if available
`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

### Details

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.

### Value

None.

### Author(s)

Xiuwen Zheng

### References

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/

### See Also

`snpgdsGDS2BED`

### Examples

    # open an example dataset (HapMap)
    genofile <- snpgdsOpen(snpgdsExampleFileName())

    # GDS ==> PED
    snpgdsGDS2PED(genofile, ped.fn="tmp")

    # close the GDS file
    snpgdsClose(genofile)

[Package SNPRelate version 1.18.1 Index]