MAplot {oligo} | R Documentation

## MA plots

### 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)
    }

[Package oligo version 1.58.0 Index]