SeqArray (version 1.12.5)

seqDelete: Delete GDS Variables

Description

Deletes variables in the SeqArray GDS file.

Usage

seqDelete(gdsfile, info.varname=character(), format.varname=character(), samp.varname=character(), verbose=TRUE)

Arguments

gdsfile

a SeqVarGDSClass object

info.varname

the variables in the INFO field, i.e., "annotation/info/VARIABLE_NAME"

format.varname

the variables in the FORMAT field, i.e., "annotation/format/VARIABLE_NAME"

samp.varname

the variables in the sample annotation field, i.e., "sample.annotation/VARIABLE_NAME"

verbose

if TRUE, show information

Value

None.

See Also

seqOpen, seqClose

Examples

# the file of VCF
vcf.fn <- seqExampleFileName("vcf")
# or vcf.fn <- "C:/YourFolder/Your_VCF_File.vcf"

# convert
seqVCF2GDS(vcf.fn, "tmp.gds")

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

seqDelete(f, info.varname=c("HM2", "AA"), format.varname="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)