seqUnitSubset: Subset and merge the units

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

Subset and merge the units

Description

Subset and merge the variant unit(s).

Usage

seqUnitCreate(idx, desp=NULL)
seqUnitSubset(units, i)
seqUnitMerge(ut1, ut2)

Arguments

idx	a list of numeric indexing vectors for specifying variants
desp	a data.frame for annotating the variant sets
units	a list of units of selected variants, with S3 class SeqUnitListClass
ut1	a list of units of selected variants, with S3 class SeqUnitListClass
ut2	a list of units of selected variants, with S3 class SeqUnitListClass
i	a numeric or logical vector for indices specifying elements

Value

The variant unit of SeqUnitListClass.

Author(s)

Xiuwen Zheng

See Also

seqUnitSlidingWindows, seqUnitFilterCond

Examples

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

# variant units via sliding windows
units <- seqUnitSlidingWindows(gdsfile)

(u1 <- seqUnitSubset(units, 1:10))
(u2 <- seqUnitSubset(units, 30:39))

seqUnitMerge(u1, u2)

seqUnitCreate(list(1:10, 20:30), data.frame(gene=c("g1", "g2")))

# close the GDS file
seqClose(gdsfile)

zhengxwen/SeqArray documentation built on Nov. 19, 2024, 1:04 p.m.