tileCount {ChIPpeakAnno} | R Documentation

## Perform overlap queries between reads and genome by windows

### Description

tileCount extends summarizeOverlaps by providing fixed window size and step to split whole genome into windows and then do queries. It will return counts in each windows.

### Usage

    tileCount(reads, genome, windowSize=1e6, step=1e6,
                          keepPartialWindow=FALSE,
                          mode=countByOverlaps, ...)

### Arguments

`reads` | A GRanges, GRangesList GAlignments, GAlignmentsList, GAlignmentPairs or BamFileList object that represents the data to be counted by `summarizeOverlaps`.
`genome` | The object from/on which to get/set the sequence information.
`windowSize` | Size of windows
`step` | Step of windows
`keepPartialWindow` | Keep last partial window or not.
`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 genome.

### 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(seqlengths = c(chr2L=7000, chr2R=10000))
        se <- tileCount(fls, genes, windowSize=1000, step=500)

[Package ChIPpeakAnno version 3.12.7 Index]