findMaxima {csaw} | R Documentation

## Find local maxima

### Description

Find the local maxima for a given set of genomic regions.

### Usage

    findMaxima(regions, range, metric, ignore.strand=TRUE)

### Arguments

`regions` | a `GRanges` object
`range` | an integer scalar specifying the range of surrounding regions to consider as local
`metric` | a numeric vector of values for which the local maxima is found
`ignore.strand` | a logical scalar indicating whether to consider the strandedness of `regions`

### Details

For each region in `regions`, this function will examine all regions within `range` on either side. It will then determine if the current region has the maximum value of `metric` across this range. A typical metric to maximize might be the sum of counts or the average abundance across all libraries.

Preferably, `regions` should contain regularly sized and spaced windows or bins, e.g., from `windowCounts`. The sensibility of using this function for arbitrary regions is left to the user. In particular, the algorithm will not support nested regions and will fail correspondingly if any are detected.

If `ignore.strand=FALSE`, the entries in `regions` are split into their separate strands. The function is run separately on the entries for each strand, and the results are collated into a single output. This may be useful for strand-specific applications.

### Value

A logical vector indicating whether each region in `regions` is a local maxima.

### Author(s)

Aaron Lun

### See Also

`windowCounts`, `aveLogCPM`

### Examples

    bamFiles <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
    data <- windowCounts(bamFiles, filter=1)
    regions <- rowRanges(data)
    metric <- edgeR::aveLogCPM(asDGEList(data))
    findMaxima(regions, range=10, metric=metric)
    findMaxima(regions, range=50, metric=metric)
    findMaxima(regions, range=100, metric=metric)

    findMaxima(regions, range=10, metric=runif(length(regions)))
    findMaxima(regions, range=50, metric=runif(length(regions)))
    findMaxima(regions, range=100, metric=runif(length(regions)))

[Package csaw version 1.24.3 Index]