summarizeOverlapsByBins {ChIPpeakAnno} | R Documentation

## Perform overlap queries between reads and genomic features by bins

### Description

summarizeOverlapsByBins extends summarizeOverlaps by providing fixed window size and step to split each feature into bins and then do queries. It will return counts by signalSummaryFUN, which applied to bins in one feature, for each feature.

### Usage

    summarizeOverlapsByBins(
      targetRegions,
      reads,
      windowSize = 50,
      step = 10,
      signalSummaryFUN = max,
      mode = countByOverlaps,
      ...
    )

### Arguments

`targetRegions` | A GRanges object of genomic regions of interest.
`reads` | A GRanges, GRangesList GAlignments, GAlignmentsList, GAlignmentPairs or BamFileList object that represents the data to be counted by `summarizeOverlaps`.
`windowSize` | Size of windows
`step` | Step of windows
`signalSummaryFUN` | function, which will be applied to the bins in each feature.
`mode` | mode can be one of the pre-defined count methods. see summarizeOverlaps. default is countByOverlaps, alia of countOverlaps(features, reads, ignore.strand=ignore.strand)
`...` | Additional arguments passed to `summarizeOverlaps`.

### Value

A RangedSummarizedExperiment object. The assays slot holds the counts, rowRanges holds the annotation from features.

### Author(s)

Jianhong Ou

### Examples

        fls <- list.files(system.file("extdata", package="GenomicAlignments"),
                      recursive=TRUE, pattern="*bam$", full=TRUE)
        names(fls) <- basename(fls)
        genes <- GRanges(
            seqnames = c(rep("chr2L", 4), rep("chr2R", 5), rep("chr3L", 2)),
            ranges = IRanges(c(1000, 3000, 4000, 7000, 2000, 3000, 3600,
                               4000, 7500, 5000, 5400),
                             width=c(rep(500, 3), 600, 900, 500, 300, 900,
                                     300, 500, 500),
                             names=letters[1:11]))
        se <- summarizeOverlapsByBins(genes, fls, windowSize=50, step=10)

[Package ChIPpeakAnno version 3.24.2 Index]