snpgdsPED2GDS {SNPRelate} | R Documentation

## 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)

[Package SNPRelate version 1.26.0 Index]