GAhier-class: Class '"GAhier"'

In hummelma/GlobalAncova: Global test for groups of variables via model comparisons

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 [e-mail]

See Also

gGlobalAncova.hierarchical

Examples

showClass("GAhier")

# see examples in documentation of gGlobalAncova.hierarchical

hummelma/GlobalAncova documentation built on Feb. 4, 2021, 8:25 a.m.