R: Convert to a SNP GDS File

seqGDS2SNP {SeqArray}

R Documentation

Convert to a SNP GDS File

Converts a SeqArray GDS file to a SNP GDS file.

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

`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

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

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

Xiuwen Zheng

# 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]