maxGap-method: Estimated max gaps
In lawremi/biovizBase: Basic graphic utilities for visualization of genomic data.

Description Usage Arguments Details Value Author(s) See Also Examples

Compute an estimated max gap information, which could be used as max.gap argument in shringkageFun.

1 2	## S4 method for signature 'GenomicRanges' maxGap(obj, ratio = 0.0025)

`obj`	GenomicRanges object
`ratio`	Multiple by the range of the provided gaps as the max gap.

This function tries to estimate an appropriate max gap to be used for creating a shrinkage function.

A numeric value

Tengfei Yin

shrinkageFun

require(GenomicRanges)
gr1 <- GRanges("chr1", IRanges(start = c(100, 300, 600),
end = c(200, 400, 800)))
gr2 <- GRanges("chr1", IRanges(start = c(100, 350, 550),
end = c(220, 500, 900)))
gaps.gr <- intersect(gaps(gr1, start = min(start(gr1))),
gaps(gr2, start = min(start(gr2))))
shrink.fun <- shrinkageFun(gaps.gr, max.gap = maxGap(gaps.gr))
shrink.fun(gr1)
shrink.fun(gr2)