Brundle: Brundle

In Brundle: Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data

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)

Brundle documentation built on May 2, 2019, 10:14 a.m.