countTable: Counting reads in features

In jianhong/diffPeaks: Quantifying Differential Features

Description

Counting reads in giving features.

Usage

countTable(features, bamfiles, colData, samples = bamfiles,
  windowSize = 200L, mode = IntersectionNotStrict, ...)

Arguments

features	an object of GRanges
bamfiles	filenames of aligned reads
colData	a DataFrame or data.frame with at least a single column. Rows of colData correspond to bamfiles
samples	names of samples, could be same length with bamfiles
windowSize	the size of windows for counts
mode	mode of counts. See summarizeOverlaps for details. Default is IntersectionNotStrict.
...	parameters could be passed to summarizeOverlaps

Value

a list of RangedSummarizedExperiment

Author(s)

Jianhong Ou

Examples

path <- system.file("extdata", package = "diffPeaks", mustWork = TRUE)
bamfiles <- dir(path, "bam$")
peaks <- dir(path, "bed$")
p <- mergePeaks(file.path(path, peaks))
colData <- DataFrame(samples=bamfiles, condition=sub(".rep..bam", "", bamfiles))
cnt <- countTable(p, file.path(path, bamfiles), colData)

jianhong/diffPeaks documentation built on May 22, 2019, 12:37 p.m.