R: Brundle

Brundle

R Documentation

Brundle

Description

Normalise one DiffBind object to a second control set of peaks.

Usage

Brundle(dbaExperiment, dbaControl, jg.treatedCondition,
  jg.untreatedCondition, jg.experimentSampleSheet, jg.controlSampleSheet,
  jg.correctionFactor = FALSE, jg.noBAMs = FALSE)

Arguments

`dbaExperiment`	DiffBind object to be normalised
`dbaControl`	DiffBind object of control peaks
`jg.treatedCondition`	Identical to treated condition in the sample sheet.
`jg.untreatedCondition`	Identical to the control condition in the sample sheet.
`jg.experimentSampleSheet`	Filename of samplesheet for experimental peaks
`jg.controlSampleSheet`	Filename of samplesheet for control peaks
`jg.correctionFactor`	Manually specify correction factor.
`jg.noBAMs`	If set to true, correction factor is estimated from the DiffBind object.

Examples

data(dbaExperiment,package="Brundle")
data(dbaControl,package="Brundle")
fpath <- system.file("extdata", "samplesheet_SLX14438_hs_ER_DBA.csv",package="Brundle")
jg.ExperimentSampleSheet<-fpath
fpath <- system.file("extdata", "samplesheet_SLX14438_hs_CTCF_DBA.csv",package="Brundle")
jg.ControlSampleSheet<-fpath
Brundle(dbaExperiment,dbaControl,"Fulvestrant","none",
         jg.ExperimentSampleSheet,jg.ControlSampleSheet,jg.noBAMs=TRUE)