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Class graphMCP

Source: R/graphMCP.R
graphMCP-class.Rd

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

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)
#>       H11       H21       H31       H12       H22       H32 
#> 0.3333333 0.3333333 0.3333333 0.0000000 0.0000000 0.0000000 

getRejected(graph)
#>   H11   H21   H31   H12   H22   H32 
#> FALSE FALSE FALSE FALSE FALSE FALSE 

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

getWeights(result@graphs[[4]])
#>       H11       H21       H31       H12       H22       H32 
#> 0.6666667 0.0000000 0.0000000 0.0000000 0.3333333 0.0000000 
getRejected(result@graphs[[4]])
#>   H11   H21   H31   H12   H22   H32 
#> FALSE  TRUE  TRUE FALSE FALSE  TRUE