findMaxima: Find local maxima

In LTLA/csaw: ChIP-Seq Analysis with Windows

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)))

LTLA/csaw documentation built on Dec. 11, 2023, 5:11 a.m.