ICod {dSimer} | R Documentation

## calculate disease similarity by ICod

### 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

    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

    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)

[Package dSimer version 1.12.0 Index]