qpGraph-class {qpgraph} | R Documentation

## The qp-graph

### Description

The `"qpGraph"` class is the class to store and manipulate q-order (partial) correlation graphs, or qp-graphs for short. See Castelo and Roverato (2006, 2009) for a mathematical and statistical definition of a qp-graph.

In earlier versions 1.x of the `qpgraph` package there was a function called `qpGraph()` to obtain a qp-graph from a matrix of non-rejection rates. This function, as it was written, has been deprecated and replaced by this class and corresponding constructor methods of the same name. The main difference with respect to earlier 1.x versions is that the argument `threshold` is now called `epsilon`, the argument `return.type` has been removed and the current version returns an object of this class `qpGraph` described in this manual page.

### Arguments

`epsilon` | maximum cutoff value met by the edges present in the qp-graph.
`topPairs` | number of edges from the top of the ranking, defined by the non-rejection rates in `nrrMatrix`, to use to form the resulting qp-graph. This parameter is incompatible with a value different from `NULL` in `epsilon`.
`pairup.i` | subset of vertices to pair up with subset `pairup.j`
`pairup.j` | subset of vertices to pair up with subset `pairup.i`
`q` | q-order employed to derive the input matrix of non-rejection rates `nrrMatrix`.
`n` | when the input matrix of non-rejection rates `nrrMatrix` has been estimated from data, this is the number of observations in the data set.

### Objects from the Class

Objects can be created by calls of the form `qpGraph(nrrMatrix, ...)` corresponding to constructor methods that take as input a matrix of non-rejection rates, calculated with `qpNrr`.

### Slots

`p`:

  number of vertices, in one-to-one correspondence with random variables.

`q`:

  order of the qp-graph, always smaller than `p-2`.

`n`:

  when the qp-graph has been estimated from data, this is the number of observations in the data set, which must be larger than `q+2`.

`epsilon`:

  maximum cutoff value of the non-rejection rate met by the edges that are present in the qp-graph.

`g`:

  undirected graph structure of the qp-graph stored as a `graphBAM-class` object.

### Methods

`qpGraph(nrrMatrix, ...)`

  Constructor method where `nrrMatrix` is a matrix of non-rejection rates.

`show(object)`

  Method to display some bits of information about the qp-graph stored in the input argument `object`.

### Author(s)

R. Castelo

### References

Castelo, R. and Roverato, A. A robust procedure for Gaussian graphical model search from microarray data with p larger than n, J. Mach. Learn. Res., 7:2621-2650, 2006.

Castelo, R. and Roverato, A. Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J. Comp. Biol., 16(2):213-227, 2009.

### See Also

`qpNrr`

[Package qpgraph version 2.20.0 Index]