summarizeOverlapsByBins {ChIPpeakAnno} | R Documentation |
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.
summarizeOverlapsByBins(targetRegions, reads, windowSize=50, step=10, signalSummaryFUN=max, mode=countByOverlaps, ...)
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 |
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 |
A RangedSummarizedExperiment object. The assays slot holds the counts, rowRanges holds the annotation from features.
Jianhong Ou
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)