ChIPComp {ChIPComp}R Documentation

Perform hypothesis testing to detect differential binding sites

Description

Perform hypothesis testing to detect differential binding sites

Usage

	ChIPComp(countSet,A,threshold=1)

Arguments

countSet

A ChIPComp object.

A

User-specified regions to fit the model. It is a bed file with three columns, named ("chr","start","end"), could be separated by space or tab.

threshold

User specified posterior probability threshold. Default is 1.

Value

A object ChIPComp contains Column chr,start,end are the binding site genomic coordinate; Column ip_c(\#condition)_r(\#replicate) indicates ChIP counts in \#replicate in \#condition; Column ct_c(\#condition)_r(\#replicate) indicates smoothing control counts in \#replicate in \#condition; Column commonPeak 1s indicate common binding sites; Column prob.post is the posterior probability for each binding site. Column pvalue.wald is the pvalue of wald test for each binding site.

Author(s)

Hao Wu<hao.wu@emory.edu>, Li Chen <li.chen@emory.edu>

Examples


	data(seqData)
	seqData=ChIPComp(seqData)


[Package ChIPComp version 1.22.0 Index]