boxplot {oligo} | R Documentation

## Boxplot

### Description

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

### Usage

    boxplot(x, ...)
    ## S4 method for signature 'FeatureSet':
    boxplot(x, which=pmindex(x), transfo=log2,
    range=0, ...)
    ## S4 method for signature 'ExpressionSet':
    boxplot(x, which=1:nrow(x), transfo=identity,
    range=0, ...)

### Arguments

`x` | a `FeatureSet`-like object or `ExpressionSet` object.
`which` | an integer vector determining which rows of 'x' should be plotted. See 'Details'.
`transfo` | a function to transform the data before plotting. See 'Details'.
`range` | this determines how far the plot whiskers extend out from the box. If 'range' is positive, the whiskers extend to the most extreme data point which is no more than 'range' times the interquartile range from the box. A value of zero causes the whiskers to extend to the data extremes.
`...` | arguments to be passed to plot

### Details

The 'which' argument should be used to subset the object to be plotted. For example, if the user wants to plot the PM probes, he should use 'which=pmindex(x)', if MM probes are to be plotted 'which=mmindex(x)'. If all probes are to be plotted 'which=1:nrow(x)'. Note that pmindex/mmindex options will not work for summarized data.

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').

### See Also

`hist`, `image`

[Package oligo version 1.8.3 Index]