SeqArray (version 1.10.1)

seqExport: 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, verbose=TRUE)

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"

verbose

if TRUE, show information

Value

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

See Also

seqVCF2GDS

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")

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


# close
seqClose(f)

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