seqSNP2GDS {SeqArray}R Documentation

Convert SNPRelate Format to SeqArray Format

Description

Converts a SNP GDS file to a SeqArray GDS file.

Usage

seqSNP2GDS(gds.fn, out.fn, storage.option="LZMA_RA",
    major.ref=TRUE, optimize=TRUE, digest=TRUE, verbose=TRUE)

Arguments

gds.fn

the file name of SNP format

out.fn

the file name, output a file of SeqArray format

storage.option

specify the storage and compression options, "LZMA_RA" to use LZMA compression algorithm with higher compression ratio compared to "ZIP_RA"

major.ref

if TRUE, use the major allele as a reference allele; otherwise, use A allele in SNP GDS file as a reference allele

optimize

if TRUE, optimize the access efficiency by calling cleanup.gds

digest

a logical value (TRUE/FALSE) or a character ("md5", "sha1", "sha256", "sha384" or "sha512"); add hash codes to the GDS file if TRUE or a digest algorithm is specified

verbose

if TRUE, show information

Value

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

Author(s)

Xiuwen Zheng

See Also

seqGDS2SNP, seqVCF2GDS, seqGDS2VCF, seqBED2GDS

Examples

library(SNPRelate)

# the GDS file
gds.fn <- snpgdsExampleFileName()

seqSNP2GDS(gds.fn, "tmp.gds")

seqSummary("tmp.gds")


# remove the temporary file
unlink("tmp.gds", force=TRUE)

[Package SeqArray version 1.18.2 Index]