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SNPRelate (version 1.6.4)

snpgdsPED2GDS: 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

Value

None.

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.

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

Run this code
# 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)

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