boxplot {oligo} | R Documentation

## Boxplot

### Description

Boxplot for observed (log-)intensities in a FeatureSet-like object (ExpressionFeatureSet, ExonFeatureSet, SnpFeatureSet, TilingFeatureSet) and ExpressionSet.

### Usage

    ## S4 method for signature 'FeatureSet'
    boxplot(x, which=c("pm", "mm", "bg", "both",
    "all"), transfo=log2, nsample=10000, target = "mps1", ...)

    ## S4 method for signature 'ExpressionSet'
    boxplot(x, which, transfo=identity, nsample=10000, ...)

### Arguments

`x` | a `FeatureSet`-like object or `ExpressionSet` object.
`which` | character defining what probe types are to be used in the plot.
`transfo` | a function to transform the data before plotting. See 'Details'.
`nsample` | number of units to sample and build the plot.
`...` | arguments to be passed to the default boxplot method.

### Details

The 'transfo' argument will set the transformation to be used. For raw data, 'transfo=log2' is a common practice. For summarized data (which are often in log2-scale), no transformation is needed (therefore 'transfo=identity').

### Note

The boxplot methods for `FeatureSet` and `Expression` use a sample (via `sample`) of the probes/probesets to produce the plot. Therefore, the user interested in reproducibility is advised to use `set.seed`.

### See Also

`hist`, `image`, `sample`, `set.seed`

[Package oligo version 1.54.1 Index]