snpgdsGDS2PED: Conversion from GDS to PED

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

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)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Converting from GDS to PLINK PED:
	Output a MAP file DONE.
	Output a PED file ...
		Output: 	Fri Apr  6 02:37:02 2018	0%
		Output: 	Fri Apr  6 02:37:02 2018	100%

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