seqUnitSlidingWindows: Sliding units of selected variants

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

Sliding units of selected variants

Description

Generates units of selected variants via sliding windows.

Usage

seqUnitSlidingWindows(gdsfile, win.size=5000L, win.shift=2500L, win.start=0L,
    dup.rm=TRUE, verbose=TRUE)

Arguments

gdsfile	a SeqVarGDSClass object
win.size	window size in basepair
win.shift	the shift of sliding window in basepair
win.start	the start position in basepair
dup.rm	if TRUE, remove duplicate and zero-length windows
verbose	if TRUE, display information

Value

A S3 object with the class name "SeqUnitListClass" and two components (desp and index): the first is a data.frame with columns "chr", "start" and "end", and the second is list of integer vectors (the variant indices).

Author(s)

Xiuwen Zheng

See Also

seqUnitApply, seqUnitFilterCond

Examples

# open the GDS file
gdsfile <- seqOpen(seqExampleFileName("gds"))

v <- seqUnitSlidingWindows(gdsfile)
v  # "desp" "index"

# close the GDS file
seqClose(gdsfile)

zhengxwen/SeqArray documentation built on Dec. 14, 2024, 8:36 p.m.