MAplot-methods: MA plots

In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays

Description

Create MA plots using a reference array (if one channel) or using channel2 as reference (if two channel).

Usage

MAplot(object, ...)

## S4 method for signature 'FeatureSet'
MAplot(object, what=pm, transfo=log2, groups,
       refSamples, which, pch=".", summaryFun=rowMedians,
       plotFun=smoothScatter, main="vs pseudo-median reference chip",
       pairs=FALSE, ...)

## S4 method for signature 'TilingFeatureSet'
MAplot(object, what=pm, transfo=log2, groups,
       refSamples, which, pch=".", summaryFun=rowMedians,
       plotFun=smoothScatter, main="vs pseudo-median reference chip",
       pairs=FALSE, ...)

## S4 method for signature 'PLMset'
MAplot(object, what=coefs, transfo=identity, groups,
       refSamples, which, pch=".", summaryFun=rowMedians,
       plotFun=smoothScatter, main="vs pseudo-median reference chip",
       pairs=FALSE, ...)

## S4 method for signature 'matrix'
MAplot(object, what=identity, transfo=identity,
       groups, refSamples, which, pch=".", summaryFun=rowMedians,
       plotFun=smoothScatter, main="vs pseudo-median reference chip",
       pairs=FALSE, ...)

## S4 method for signature 'ExpressionSet'
MAplot(object, what=exprs, transfo=identity,
       groups, refSamples, which, pch=".", summaryFun=rowMedians,
       plotFun=smoothScatter, main="vs pseudo-median reference chip",
       pairs=FALSE, ...)

Arguments

object	FeatureSet, PLMset or ExpressionSet object.
what	function to be applied on object that will extract the statistics of interest, from which log-ratios and average log-intensities will be computed.
transfo	function to transform the data prior to plotting.
groups	factor describing groups of samples that will be combined prior to plotting. If missing, MvA plots are done per sample.
refSamples	integers (indexing samples) to define which subjects will be used to compute the reference set. If missing, a pseudo-reference chip is estimated using summaryFun.
which	integer (indexing samples) describing which samples are to be plotted.
pch	same as pch in plot
summaryFun	function that operates on a matrix and returns a vector that will be used to summarize data belonging to the same group (or reference) on the computation of grouped-stats.
plotFun	function to be used for plotting. Usually smoothScatter, plot or points.
main	string to be used in title.
pairs	logical flag to determine if a matrix of MvA plots is to be generated
...	Other arguments to be passed downstream, like plot arguments.

Details

MAplot will take the following extra arguments:

1. subset: indices of elements to be plotted to reduce impact of plotting 100's thousands points (if pairs=FALSE only);

2. span: see loess;

3. family.loess: see loess;

4. addLoess: logical flag (default TRUE) to add a loess estimate;

5. parParams: list of params to be passed to par() (if pairs=TRUE only);

Value

Plot

Author(s)

Benilton Carvalho - based on Ben Bolstad's original MAplot function.

See Also

plot, smoothScatter

Examples

if(require(oligoData) & require(pd.hg18.60mer.expr)){
  data(nimbleExpressionFS)
  nimbleExpressionFS
  groups <- factor(rep(c('brain', 'UnivRef'), each=3))
  data.frame(sampleNames(nimbleExpressionFS), groups)
  MAplot(nimbleExpressionFS, pairs=TRUE, ylim=c(-.5, .5), groups=groups)
}

jmacdon/oligo documentation built on Aug. 11, 2020, 12:32 a.m.