snpgdsPED2GDS: Conversion from PLINK PED to GDS

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

Conversion from PLINK PED to GDS

Description

Convert a PLINK PED text file to a GDS file.

Usage

snpgdsPED2GDS(ped.fn, map.fn, out.gdsfn, family=TRUE, snpfirstdim=FALSE,
    compress.annotation="ZIP_RA.max", compress.geno="", verbose=TRUE)

Arguments

ped.fn	the file name of PED file, genotype information
map.fn	the file name of MAP file
out.gdsfn	the output GDS file
family	if TRUE, to include family information in the sample annotation
snpfirstdim	if TRUE, genotypes are stored in the individual-major mode, (i.e, list all SNPs for the first individual, and then list all SNPs for the second individual, etc)
compress.annotation	the compression method for the GDS variables, except "genotype"; optional values are defined in the function add.gdsn
compress.geno	the compression method for "genotype"; optional values are defined in the function add.gdsn
verbose	if TRUE, show information

Details

GDS – Genomic Data Structures, the extended file name used for storing genetic data, and the file format is used in the gdsfmt package.

PED – PLINK 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.

See Also

snpgdsGDS2PED, snpgdsBED2GDS, snpgdsGDS2BED

Examples

# open
genofile <- snpgdsOpen(snpgdsExampleFileName())

snpgdsGDS2PED(genofile, "tmp")

# close
snpgdsClose(genofile)


# PED ==> GDS
snpgdsPED2GDS("tmp.ped", "tmp.map", "test.gds")


# delete the temporary file
unlink(c("tmp.ped", "tmp.map", "test.gds"), force=TRUE)

zhengxwen/SNPRelate documentation built on Nov. 19, 2024, 1:02 p.m.