tileCount: Perform overlap queries between reads and genome by windows

Description Usage Arguments Value 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 window.

Usage

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tileCount(reads, genome, windowSize = 100000L, step = 10000L,
  mode = countByOverlaps, dataOverSamples = FALSE, ...)

Arguments

reads

A GRanges, GRangesList (should be one read per list element), 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

numeric(1) or integer(1). Size of windows.

step

numeric(1) or integer(1). Step of windows.

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)

dataOverSamples

logical(1). Data over several samples when use GRangesList as input?

...

Additional arguments passed to summarizeOverlaps.

Value

A RangedSummarizedExperiment object. The assays slot holds the counts, rowRanges holds the annotation from sliding widows of genome.

Examples

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## Not run: 
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)

## End(Not run)

##
genome <- GRanges("chr1", IRanges(1, 1))
seqlengths(genome) <- c(chr1=1000)
reads <- GRanges("chr1", IRanges((seq_len(90))*10, width=10))
tileCount(reads, genome, windowSize=100, step=50)

Bioconductor-mirror/NADfinder documentation built on July 28, 2017, 4:27 a.m.