seqDelete: Delete GDS Variables

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

Description

Deletes variables in the SeqArray GDS file.

Usage

seqDelete(gdsfile, info.var=character(), fmt.var=character(),
    samp.var=character(), verbose=TRUE)

Arguments

gdsfile	a SeqVarGDSClass object
info.var	the variables in the INFO field, i.e., "annotation/info/VARIABLE_NAME"
fmt.var	the variables in the FORMAT field, i.e., "annotation/format/VARIABLE_NAME"
samp.var	the variables in the sample annotation field, i.e., "sample.annotation/VARIABLE_NAME"
verbose	if TRUE, show information

Value

None.

Author(s)

Xiuwen Zheng

See Also

seqOpen, seqClose

Examples

# the file of GDS
gds.fn <- seqExampleFileName("gds")
file.copy(gds.fn, "tmp.gds", overwrite=TRUE)

# display
(f <- seqOpen("tmp.gds", FALSE))

seqDelete(f, info.var=c("HM2", "AA"), fmt.var="DP")
f

# close the GDS file
seqClose(f)

# clean up the fragments, reduce the file size
cleanup.gds("tmp.gds")


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

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