SeqArray (version 1.12.5)

seqSNP2GDS: 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="ZIP_RA", 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, by default seqStorageOption("ZIP_RA"); or "LZMA_RA" to use LZMZ compression algorithm with higher compression ratio

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.

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)