biovizBase (version 1.20.0)

maxGap-method: Estimated max gaps

Description

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

Usage

"maxGap"(obj, ratio = 0.0025)

Arguments

obj

GenomicRanges object

ratio

Multiple by the range of the provided gaps as the max gap.

Value

Details

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

See Also

shrinkageFun

Examples

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)