DEpeaks: differential binding analysis

In jianhong/diffPeaks: Quantifying Differential Features

Description

use DEseq2 to test differential peaks

Usage

DEpeaks(counts, ...)

Arguments

counts	output of countTable
...	parameters could be passed to DESeqDataSet

Value

an object of GRanges

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)
DEpeaks(cnt, design= ~condition)

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