seqResetVariantID: Reset Variant ID in SeqArray GDS Files

In zhengxwen/SeqArray: Data management of large-scale whole-genome sequence variant calls using GDS files

Reset Variant ID in SeqArray GDS Files

Description

Resets the variant IDs in multiple SeqArray GDS files.

Usage

seqResetVariantID(gds.fn, start=1L, set=NULL, digest=TRUE, optimize=TRUE,
    verbose=TRUE)

Arguments

gds.fn	a character vector of multiple GDS file names
start	the starting number of the sequence of variant IDs
set	NULL or a logical vector; NULL for resetting all files, or TRUE for resetting variant.id for that GDS file
digest	a logical value, if TRUE, add a md5 hash code
optimize	if TRUE, optimize the access efficiency by calling cleanup.gds
verbose	if TRUE, show information

Details

The variant IDs will be replaced by the numbers in sequential order and adjacent to each file. The variant ID starts from start (1 by default) in the first GDS file.

Value

None.

Author(s)

Xiuwen Zheng

See Also

seqVCF2GDS

Examples

fn <- seqExampleFileName("gds")

file.copy(fn, "tmp1.gds", overwrite=TRUE)
file.copy(fn, "tmp2.gds", overwrite=TRUE)

gds.fn <- c("tmp1.gds", "tmp2.gds")
seqResetVariantID(gds.fn)

f <- seqOpen("tmp1.gds")
head(seqGetData(f, "variant.id"))
seqClose(f)

f <- seqOpen("tmp2.gds")
head(seqGetData(f, "variant.id"))
seqClose(f)


# delete the temporary files
unlink(gds.fn, force=TRUE)

zhengxwen/SeqArray documentation built on April 14, 2025, 2:19 a.m.