seqUnitSlidingWindows: Sliding units of selected variants In SeqArray: Data management of large-scale whole-genome sequence variant calls Description Usage Arguments Value Author(s) See Also Examples
Description
Generates units of selected variants via sliding windows.
Usage
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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
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# open the GDS file gdsfile <- seqOpen(seqExampleFileName("gds")) v <- seqUnitSlidingWindows(gdsfile) v # "desp" "index" # close the GDS file seqClose(gdsfile)
SeqArray documentation built on Nov. 8, 2020, 5:08 p.m.
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Description Usage Arguments Value Author(s) See Also Examples
Description
Generates units of selected variants via sliding windows.
Usage
1 2 | seqUnitSlidingWindows(gdsfile, win.size=5000L, win.shift=2500L, win.start=0L, dup.rm=TRUE, verbose=TRUE) |
Arguments
gdsfile | a |
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 |
verbose | if |
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
1 2 3 4 5 6 7 8 | # open the GDS file gdsfile <- seqOpen(seqExampleFileName("gds")) v <- seqUnitSlidingWindows(gdsfile) v # "desp" "index" # close the GDS file seqClose(gdsfile) |
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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