HDP.ranking {GSAR} | R Documentation

## High Directed Preorder Ranking of MST

### Description

Rank nodes in an object of class `igraph` (see package `igraph` for the definition of class `igraph`) containing a minimum spanning tree (MST) according to the High Directed Preorder traversal of the tree.

### Usage

    HDP.ranking(object)

### Arguments

`object` | object of class `igraph` that consists of a minimum spanning tree.

### Details

Rank nodes in an object of class `igraph` (see package `igraph`) containing a minimum spanning tree (MST). The MST is rooted at a node with the largest geodesic distance and the rest of the nodes are ranked according to the high directed preorder (HDP) traversal of the tree (Friedman and Rafsky 1979).

### Value

Numeric vector giving the node ranks according to HDP traversal of the MST.

### Note

This function does not work properly if there is any node in the MST with more than 26 links. However, this situation is almost impossible for a dataset composed of a few hundreds or less of samples.

### Author(s)

Yasir Rahmatallah and Galina Glazko

### References

Rahmatallah Y., Emmert-Streib F. and Glazko G. (2012) Gene set analysis for self-contained tests: complex null and specific alternative hypotheses. Bioinformatics 28, 3073–3080.

Friedman J. and Rafsky L. (1979) Multivariate generalization of the Wald-Wolfowitz and Smirnov two-sample tests. Ann. Stat. 7, 697–717.

### See Also

`radial.ranking`, `KStest`, `MDtest`.

### Examples

    ## generate random data using normal distribution
    ## generate 20 features in 20 samples
    object <- matrix(rnorm(400),20,20)
    objt <- aperm(object, c(2,1))
    ## calculate the weight matrix
    Wmat <- as.matrix(dist(objt, method = "euclidean", diag = TRUE, upper = TRUE, p = 2))
    ## create a weighted undirectional graph from the weight matrix
    gr <- graph_from_adjacency_matrix(Wmat, weighted = TRUE, mode = "undirected")
    ## find the minimum spanning tree
    MST <- mst(gr)
    HDP.ranks <- HDP.ranking(MST)

[Package GSAR version 1.14.0 Index]