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)

[Package biovizBase version 1.40.0 Index]