CMHpeaks: differential binding analysis by Cochran-Mantel-Haenszel Test

In jianhong/diffPeaks: Quantifying Differential Features

Description

use Cochran-Mantel-Haenszel Test to test differential peaks

Usage

CMHpeaks(counts, conditionA, conditionB, ...)

Arguments

counts	output of countTable
conditionA, conditionB	condition A and B. Comparison will be A-B.
...	not used.

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), 
                     pairs=rep(c(1,2,3), 2))
cnt <- countTable(p, file.path(path, bamfiles), colData)
CMHpeaks(cnt, conditionA="inj", conditionB="uni")

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