seqGDS2SNP: Convert to a SNP GDS File

In SeqArray: Data management of large-scale whole-genome sequence variant calls

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")

SeqArray documentation built on Nov. 8, 2020, 5:08 p.m.