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="LZMA_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 1.20.2 Index]