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)


[Package Brundle version 1.0.9 Index]