SeqArray (version 1.12.5)

seqGDS2SNP: 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

Value

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

Details

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

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")