shrinkageFun-method: Shrinkage function

Description Usage Arguments Details Value Author(s) Examples

Description

Create a shrinkage function based on specified gaps and shrinkage rate.

Usage

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## For IRanges
## S4 method for signature 'IRanges'
shrinkageFun(obj, max.gap = 1L)

## For GenomicRanges
## S4 method for signature 'GenomicRanges'
shrinkageFun(obj, max.gap = 1L)

is_coord_truncate_gaps(obj)

Arguments

obj

GenomicRanges object which represent gaps

max.gap

Gaps to be kept, it's a fixed value, if this value is bigger than certain gap interval, then that gap is not going to be shrunk.

Details

shrinkageFun function will read in a GenomicRanges object which represent the gaps, and return a function which works for another GenomicRanges object, to shrink that object based on previously specified gaps shrinking information. You could use this function to treat multiple tracks(e.g. GRanges) to make sure they shrunk based on the common gaps and the same ratio.

is_coord_truncate_gaps is used to check if a GRanges object is in "truncate_gaps" coordiantes or not.

Value

A shrinkage function which could shrink a GenomicRanges object, this function will add coord "truncate_gaps" and max.gap to metadata, ".ori" for oringal data as extra column

Author(s)

Michael Lawrence, Tengfei Yin

Examples

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library(GenomicRanges)
gr1 <- GRanges("chr1", IRanges(start = c(100, 300, 600),
                               end = c(200, 400, 800)))

shrink.fun1 <- shrinkageFun(gaps(gr1), max.gap = maxGap(gaps(gr1), 0.1))
shrink.fun2 <- shrinkageFun(gaps(gr1, start(gr1), end(gr1)), max.gap = maxGap(gaps(gr1), 0.1))
shrink.fun3 <- shrinkageFun(gaps(gr1), max.gap = 0)
s1 <- shrink.fun1(gr1)
s2 <- shrink.fun2(gr1)
s3 <- shrink.fun3(gr1)
metadata(s1)$coord
values(s1)$.ori
is_coord_truncate_gaps(s1)

Bioconductor-mirror/biovizBase documentation built on June 1, 2017, 5:21 a.m.