ICod: calculate disease similarity by ICod

Description Usage Arguments Value Author(s) References Examples

View source: R/ICod.R

Description

given two vectors of diseases, a list of disease-gene associations and a PPI neteork, this function will calculate disease similarity by method ICod

Usage

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ICod(D1, D2, d2g, graph, A = 0.9, b = 1, C = 0)

Arguments

D1

a vector consists disease ids

D2

another vector consists disease ids

d2g

a list of disease-gene associations

graph

an igraph graph object of PPI network

A

a parameter used in ICod to calculate transformed distance of node pair, default 0.9

b

a parameter used in ICod to calculate transformed distance of node pair, default 1

C

a parameter used in ICod to calculate disease similarity, default 0

Value

a matrix of disease disease simialrity which rownames is D1 and colnames is D2

Author(s)

Peng Ni, Min Li

References

Paik H, Heo HS, Ban H, et al. Unraveling human protein interaction networks underlying co-occurrences of diseases and pathological conditions[J]. Journal of translational medicine, 2014, 12(1): 99.

Examples

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data(d2g_fundo_symbol)
data(PPI_HPRD)

graph_hprd<-graph.data.frame(PPI_HPRD,directed=FALSE) #get a igraph object based on HPRD data
ds<-sample(names(d2g_fundo_symbol),5)
ICod(ds,ds,d2g_fundo_symbol,graph_hprd)

dSimer documentation built on Nov. 17, 2017, 12:51 p.m.