maplots: Function to construct the classic MA plots from a dataset

In markdunning/beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

Description

Note that a ggplot2 object is returned, which can be modified programatically.

The default operation is to construct a reference array be averaging all probes across the whole datasets, and then making an MA plot by comparing each array to this reference. A log2 transformation is performed, but this can be turned-off by setting do.log=FALSE.

Alternatively, a SampleGroup may be specified. This is a character string that should match a column in the phenoData for the object. Then, the resulting MA plot will contain all pairwise comparisons between samples belonging to the same group. A list of ggplot objects is returned, each item in the list being a different group.

Details

Densities are computed using the 'hexbin' package

Value

A list of ggplot2 objects is returned.

Author(s)

Mark Dunning

Examples

if(require(beadarrayExampleData)){
data(exampleSummaryData)
rawdata <- channel(exampleSummaryData, "G")
 mas <- plotMA(rawdata,do.log=FALSE)
mas
##Smoothed lines can be added
mas + geom_smooth(col="red")
##Added lines on the y axis
mas + geom_hline(yintercept=c(-1.5,1.5),col="red")
##Changing the color scale
mas + scale_fill_gradient2(low="yellow",mid="orange",high="red")

mas <- plotMA(rawdata,do.log=FALSE,SampleGroup="SampleFac")
mas[[1]]
mas[[2]]

}

markdunning/beadarray documentation built on May 9, 2019, 8:35 a.m.