seqExport: Export to a GDS File

In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Export to a GDS File

Description

Exports to a GDS file with selected samples and variants, which are defined by seqSetFilter().

Usage

seqExport(gdsfile, out.fn, info.var=NULL, fmt.var=NULL, samp.var=NULL,
    optimize=TRUE, digest=TRUE, verbose=TRUE, verbose.clean=NA)

Arguments

gdsfile	a SeqVarGDSClass object
out.fn	the file name of output GDS file
info.var	characters, the variable name(s) in the INFO field for import; or NULL for all variables
fmt.var	characters, the variable name(s) in the FORMAT field for import; or NULL for all variables
samp.var	characters, the variable name(s) in the folder "sample.annotation"
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 md5 hash codes to the GDS file if TRUE or a digest algorithm is specified
verbose	if TRUE, show information
verbose.clean	when verbose.clean=NA, set it to verbose; whether display information when calling cleanup.gds or not; only applicable when optimize=TRUE

Value

Return the file name of GDS format with an absolute path.

Author(s)

Xiuwen Zheng

See Also

seqVCF2GDS, cleanup.gds

Examples

# open the GDS file
(gds.fn <- seqExampleFileName("gds"))
(f <- seqOpen(gds.fn))

# get 'sample.id'
head(samp.id <- seqGetData(f, "sample.id"))

# get 'variant.id'
head(variant.id <- seqGetData(f, "variant.id"))

set.seed(100)
# set sample and variant filters
seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10,12,14,16)])
seqSetFilter(f, variant.id=sample(variant.id, 100))


# export
seqExport(f, "tmp.gds")
seqExport(f, "tmp.gds", info.var=character())
seqExport(f, "tmp.gds", fmt.var=character())
seqExport(f, "tmp.gds", samp.var=character())


# show file
(f1 <- seqOpen("tmp.gds")); seqClose(f1)


# close
seqClose(f)

# delete the temporary file
unlink("tmp.gds")

zhengxwen/SeqArray documentation built on May 1, 2024, 6:26 p.m.