tileCount {ChIPpeakAnno} | R Documentation |
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.
tileCount(reads, genome, windowSize=1e6, step=1e6, keepPartialWindow=FALSE, mode=countByOverlaps, ...)
reads |
A GRanges, GRangesList
GAlignments,
GAlignmentsList,
GAlignmentPairs or
BamFileList object that represents the data to be
counted by |
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 |
A RangedSummarizedExperiment object. The assays slot holds the counts, rowRanges holds the annotation from genome.
Jianhong Ou
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)