seqBED2GDS {SeqArray} | R Documentation

## Convert PLINK BED Format to SeqArray Format

### Description

Converts a PLINK BED file to a SeqArray GDS file.

### Usage

    seqBED2GDS(bed.fn, fam.fn, bim.fn, out.gdsfn,
        compress.geno="LZMA_RA", compress.annotation="LZMA_RA",
        optimize=TRUE, digest=TRUE, verbose=TRUE)

### Arguments

`bed.fn` | the file name of binary file, genotype information
`fam.fn` | the file name of first six columns of `".ped"`
`bim.fn` | the file name of extended MAP file: two extra columns = allele names
`out.gdsfn` | the file name, output a file of SeqArray format
`compress.geno` | the compression method for "genotype"; optional values are defined in the function `add.gdsn`
`compress.annotation` | the compression method for the GDS variables, except "genotype"; optional values are defined in the function `add.gdsn`
`optimize` | if `TRUE`, optimize the access efficiency by calling `cleanup.gds`
`digest` | a logical value (TRUE/FALSE) or a character ("md5", "sha1", "sha256", "sha384" or "sha512"); add hash codes to the GDS file if TRUE or a digest algorithm is specified
`verbose` | if `TRUE`, show information

### Value

Return the file name of SeqArray file with an absolute path.

### Author(s)

Xiuwen Zheng

### See Also

`seqSNP2GDS`, `seqVCF2GDS`

### Examples

    library(SNPRelate)

    # PLINK BED files
    bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate")
    fam.fn <- system.file("extdata", "plinkhapmap.fam.gz", package="SNPRelate")
    bim.fn <- system.file("extdata", "plinkhapmap.bim.gz", package="SNPRelate")

    # convert
    seqBED2GDS(bed.fn, fam.fn, bim.fn, "tmp.gds")

    seqSummary("tmp.gds")

    # remove the temporary file
    unlink("tmp.gds", force=TRUE)

[Package SeqArray version 1.26.2 Index]