tileCount: Perform overlap queries between reads and genome by windows

Description Usage Arguments Value Author(s) Examples

View source: R/tileCount.R

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

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tileCount(
  reads,
  genome,
  windowSize = 1e+06,
  step = 1e+06,
  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

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    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)

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.