oligo (version 1.36.1)

MAplot: MA plots

Description

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

Usage

MAplot(object, ...)
## S3 method for class 'FeatureSet':
MAplot(object, what=pm, transfo=log2, groups,
       refSamples, which, pch=".", summaryFun=rowMedians,
       plotFun=smoothScatter, main="vs pseudo-median reference chip",
       pairs=FALSE, ...)
## S3 method for class 'TilingFeatureSet':
MAplot(object, what=pm, transfo=log2, groups,
       refSamples, which, pch=".", summaryFun=rowMedians,
       plotFun=smoothScatter, main="vs pseudo-median reference chip",
       pairs=FALSE, ...)
## S3 method for class 'PLMset':
MAplot(object, what=coefs, transfo=identity, groups,
       refSamples, which, pch=".", summaryFun=rowMedians,
       plotFun=smoothScatter, main="vs pseudo-median reference chip",
       pairs=FALSE, ...)
## S3 method for class 'matrix':
MAplot(object, what=identity, transfo=identity,
       groups, refSamples, which, pch=".", summaryFun=rowMedians,
       plotFun=smoothScatter, main="vs pseudo-median reference chip",
       pairs=FALSE, ...)
## S3 method for class '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.

Value

• Plot

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: seeloess;
3. family.loess: seeloess;
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);

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)
}