ICod: calculate disease similarity by ICod
In dSimer: Integration of Disease Similarity Methods

Description Usage Arguments Value Author(s) References Examples

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

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

`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

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

Peng Ni, Min Li

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.

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)