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, dosage=FALSE, compress.geno="LZMA_RA",
        compress.annotation="LZMA_RA", ds.type=c("packedreal16", "float", "double"),
        optimize=TRUE, verbose=TRUE)

### Arguments

`gdsfile` | character (a GDS file name), or a `SeqVarGDSClass` object
`out.gdsfn` | the file name, output a file of VCF format
`dosage` | a logical value, or characters for the variable name of dosage in the SeqArray file; if `FALSE` exports genotypes, otherwise exports dosages
`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`
`ds.type` | applicable when import dosages, the data type for storing dosages; see `add.gdsn`; `ds.type="packedreal16"` by default
`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 1.30.0 Index]