maxGap-method {biovizBase}

R Documentation

Estimated max gaps

Description

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

Usage

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

Arguments

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

Details

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

Value

A numeric value

Author(s)

Tengfei Yin

See Also

shrinkageFun

Examples

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)

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