jg.plotMA: jg.plotMA

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

Description

This function plots both the control and experimental data on an MA plot. It also allows for the user to provide a normalisation coefficient for the data.

Usage

jg.plotMA(jg.experimentPeakset, jg.controlPeakset, jg.untreatedNames,
  jg.treatedNames, jg.coefficient)

Arguments

jg.experimentPeakset	is the peakset of the experimental data extracted from a DiffBind ojbect with jg.dbaGetPeakset
jg.controlPeakset	is the peakset of the control data extracted from a DiffBind ojbect with jg.dbaGetPeakset
jg.untreatedNames	is a list of sample names for the control or untreated conditions
jg.treatedNames	is a list of sample samples for the treated conditions
jg.coefficient	is a normalisation coefficient for the data that can be generated via the pipeline. Can be set to 1 to view before normalisation.

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