Sun_topology {dSimer} | R Documentation

## Sun's topology measure of disease similarity calculating

### Description

given two vectors of diseases, a list of disease-gene associations, a matrix of genes' graphlet signature in a PPI network and a weight vector of 73 orbits in graphlet theory, this function will calculate disease similarity by method Sun_function

### Usage

    Sun_topology(D1, D2, d2g, graphlet_sig_mat, weight)

### Arguments

`D1` | a vector consists disease ids
`D2` | another vector consists disease ids
`d2g` | a list of disease-gene associations
`graphlet_sig_mat` | matrix of graphlet signature of nodes in a ppi network calculated by orca, see examples below.
`weight` | a vector which elements are weight factors to each orbit in graphlet theory

### Value

a disease disease similarity matrix

### Author(s)

Peng Ni, Min Li

### References

Sun K, Goncalves JP, Larminie C. Predicting disease associations via biological network analysis[J]. BMC bioinformatics, 2014, 15(1): 304.

### Examples

    data(d2g_fundo_symbol)
    data(graphlet_sig_hprd) #get graphlet signatures of genes in HPRD PPI network
    data(weight)
    ds<-sample(names(d2g_fundo_symbol),5)
    Sun_topology(ds,ds,d2g_fundo_symbol,graphlet_sig_hprd,weight)

[Package dSimer version 1.6.0 Index]