DBFpeaks: differential binding analysis

Description Usage Arguments Value Author(s) Examples

View source: R/DBFpeaks.R

Description

use DBF to test differential peaks

Usage

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DBFpeaks(counts, ...)

Arguments

counts

output of countTable

...

parameters could be passed to DESeqDataSet

Value

an list of GRanges

Author(s)

Jianhong Ou

Examples

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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)
DBFpeaks(cnt, design= ~condition)

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