tileCount: Perform overlap queries between reads and genome by windows

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

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 = 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

    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)

jianhong/ChIPpeakAnno documentation built on April 28, 2024, 3:10 p.m.