seqGDS2SNP {SeqArray} | R Documentation

## Convert to a SNP GDS File

### Description

Converts a SeqArray GDS file to a SNP GDS file.

### Usage

    seqGDS2SNP(gdsfile, out.gdsfn, compress.geno="ZIP_RA",
        compress.annotation="ZIP_RA", optimize=TRUE, verbose=TRUE)

### Arguments

`gdsfile` | character (GDS file name), or a `SeqVarGDSClass` object
`out.gdsfn` | the file name, output a file of VCF 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`
`verbose` | if `TRUE`, show information

### Details

`seqSetFilter` can be used to define a subset of data for the conversion.

### Value

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

### Author(s)

Xiuwen Zheng

### See Also

`seqSNP2GDS`, `seqVCF2GDS`, `seqGDS2VCF`

### Examples

    # the GDS file
    gds.fn <- seqExampleFileName("gds")

    seqGDS2SNP(gds.fn, "tmp.gds")

    # delete the temporary file
    unlink("tmp.gds")

[Package SeqArray version 1.18.2 Index]