GAhier class {GlobalAncova} | R Documentation

## Class `"GAhier"`

### Description

Class for storing results of hierarchical testing procedure performed by `gGlobalAncova.hierarchical`

### Usage

    ## S4 method for signature 'GAhier'
    show(object)
    ## S4 method for signature 'GAhier'
    results(object)
    ## S4 method for signature 'GAhier'
    sigEndnodes(object, onlySingleton=FALSE)
    ## S4 method for signature 'GAhier'
    Plot.hierarchy(object, dend, col=1:2, lwd=1:2, collab, returndend=FALSE, cex.labels=1.5, ...)

### Arguments

`object` | object of class `GAhier`
`onlySingleton` | if `TRUE`, only names of singleton variables within the significant nodes are returned
`dend` | `dendrogram` object specifying the hierarchy of the variables
`col` | colors for significant and non-significant nodes and branches, respectively
`lwd` | line width for branches to non-significant and significant nodes, respectively
`collab` | vector of colors for coloring dendrogram leave labels (can be independent of significant/non-significant nodes); has to be named according to variable names; if missing, significant and non-significant variables are colored using colors defined in `col`
`returndend` | if `TRUE`, updated `dendrogram` object is returned (e.g. for use in further plots)
`cex.labels` | size of leave labels
`...` | further graphical parameters, passed to `plot.dendrogram`

### Slots

`clustervariables`:

  Object of class `"list"` containing names of variables in each tested cluster

`p.values`:

  Object of class `"list"` containing p-values for each tested cluster

`alpha`:

  Object of class `"numeric"`; chosen global significance level; if `K` had been specified, this additionally contains the adjusted significance levels for the `K` sub-hierarchies

`n.variables`:

  Object of class `"numeric"`; number of variables in total

`permstats`:

  Object of class `"matrixOrNULL"`; if `returnPermstats` had been set to `TRUE`, this is a matrix containing individual statistics for all variables for all permutations, otherwise `NULL`

### Methods

show

  `signature(object = "GAhier")`: Show general information and significant end nodes

results

  `signature(object = "GAhier")`: Get a `data.frame` with significant end nodes, number and names of variables included in each node and corresponding p-value

sigEndnodes

  `signature(object = "GAhier")`: Get names of signficant end nodes

Plot.hierarchy

  `signature(object = "GAhier")`: Plot hierarchy dendrogram, where significant nodes (and branches to those nodes) are highlighted

### Note

Coloring the dendrogram in `Plot.hierarchy` is based on functionality from the globaltest package

### Author(s)

Manuela Hummel m.hummel@dkfz.de

### See Also

`gGlobalAncova.hierarchical`

### Examples

    showClass("GAhier")

    # see examples in documentation of gGlobalAncova.hierarchical

[Package GlobalAncova version 4.2.0 Index]