mboxplot-methods {xps} | R Documentation

## Box Plots of Relative M Values

### Description

Produce boxplots of relative M values for the set of arrays.

Usage

`mboxplot(x, which = "", size = 0, transfo = log2, method = "mean", range = 0, ylim = c(-1,1), outline = FALSE, names = "namepart", ...)`

### Arguments

`x` | object of class `DataTreeSet` or `ExprTreeSet`.
`which` | type of probes to be used, for details see `validData`.
`size` | length of sequence to be generated as subset.
`transfo` | a valid function to transform the data, usually “log2”, or “0”.
`method` | method to create the reference data, “mean” or “median”.
`range` | determines how far the plot whiskers extend out from the box.
`ylim` | range for the plotted y values.
`outline` | if `outline` is not true, the outliers are not drawn.
`names` | optional vector of sample names.
`...` | optional arguments to be passed to `boxplot`.

### Details

Create boxplots of M plots, where M is determined relative to a pseudo-mean reference chip.

For `names=NULL` full column names of slot `data` will be displayed while for `names="namepart"` column names will be displayed without name extension. If `names` is a vector of column names, only these columns will displayed as boxplot.

### Note

For a `DataTreeSet` object, data must first be attached using method `attachInten`.

### Author(s)

Christian Stratowa

### See Also

`boxplot.dev`, `boxplot`

### Examples

    # load existing ROOT scheme file and ROOT data file
    scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
    data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

    # need to attach scheme mask and probe intensities
    data.test3 <- attachMask(data.test3)
    data.test3 <- attachInten(data.test3)

    if (interactive()) {
    mboxplot(data.test3, ylim=c(-6,6))
    }

    # optionally remove mask and data to free memory
    data.test3 <- removeInten(data.test3)
    data.test3 <- removeMask(data.test3)

[Package xps version 1.0.2 Index]