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
```