Sun_topology {dSimer} | R Documentation |
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
Sun_topology(D1, D2, d2g, graphlet_sig_mat, weight)
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 |
a disease disease similarity matrix
Peng Ni, Min Li
Sun K, Goncalves JP, Larminie C. Predicting disease associations via biological network analysis[J]. BMC bioinformatics, 2014, 15(1): 304.
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)