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 1.10.0 Index]