graphMCP-class: Class graphMCP
In gMCPLite: Lightweight Graph Based Multiple Comparison Procedures

graphMCP-class

R Documentation

Class graphMCP

Description

A graphMCP object describes a sequentially rejective multiple test procedure.

Slots

m: A transition matrix. Can be either numerical or character depending whether the matrix contains variables or not. Row and column names will be the names of the nodes.
weights: A numeric.
edgeAttr: A list for edge attributes.
nodeAttr: A list for node attributes.

Methods

getMatrix: signature(object = "graphMCP"): A method for getting the transition matrix of the graph.
getWeights: signature(object = "graphMCP"): A method for getting the weights. If a third optional argument node is specified, only for these nodes the weight will be returned.
setWeights: signature(object = "graphMCP"): A method for setting the weights. If a third optional argument node is specified, only for these nodes the weight will be set.
getRejected: signature(object = "graphMCP"): A method for getting the information whether the hypotheses are marked in the graph as already rejected. If a second optional argument node is specified, only for these nodes the boolean vector will be returned.
getXCoordinates: signature(object = "graphMCP"): A method for getting the x coordinates of the graph. If a second optional argument node is specified, only for these nodes the x coordinates will be returned. If x coordinates are not set yet NULL is returned.
getYCoordinates: signature(object = "graphMCP"): A method for getting the y coordinates of the graph If a second optional argument node is specified, only for these nodes the x coordinates will be returned. If y coordinates are not set yet NULL is returned.
setEdge: signature(from="character", to="character", graph="graphNEL", weights="numeric"): A method for adding new edges with the given weights.
setEdge: signature(from="character", to="character", graph="graphMCP", weights="character"): A method for adding new edges with the given weights.

Author(s)

Kornelius Rohmeyer rohmeyer@small-projects.de

Examples

m <- rbind(H11=c(0,   0.5, 0,   0.5, 0,   0  ),
			H21=c(1/3, 0,   1/3, 0,   1/3, 0  ),
			H31=c(0,   0.5, 0,   0,   0,   0.5),
			H12=c(0,   1,   0,   0,   0,   0  ),
			H22=c(0.5, 0,   0.5, 0,   0,   0  ),
			H32=c(0,   1,   0,   0,   0,   0  ))

weights <- c(1/3, 1/3, 1/3, 0, 0, 0)

# Graph creation
graph <- new("graphMCP", m=m, weights=weights)

# Visualization settings
nodeX <- rep(c(100, 300, 500), 2)
nodeY <- rep(c(100, 300), each=3)
graph@nodeAttr$X <- nodeX
graph@nodeAttr$Y <- nodeY

getWeights(graph)

getRejected(graph)

pvalues <- c(0.1, 0.008, 0.005, 0.15, 0.04, 0.006)
result <- gMCP(graph, pvalues)

getWeights(result@graphs[[4]])
getRejected(result@graphs[[4]])

gMCPLite documentation built on May 29, 2024, 7:38 a.m.