FunSim {dSimer} | R Documentation

## calculate disease similarity by FunSim

### Description

given two vectors of diseases, a list of disease-gene associations , and a list of gene-gene log-likelihood score from HumanNet, this function will calculate disease similarity by method FunSim

### Usage

    FunSim(D1, D2, d2g, LLSnList)

### Arguments

`D1` | a vector consists disease ids
`D2` | another vector consists disease ids
`d2g` | a list of disease-gene associations, while gene ids should be entrez id.
`LLSnList` | a list of gene-gene log-likelihood score from HumanNet

### Value

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

### Author(s)

Peng Ni, Min Li

### References

Cheng L, Li J, Ju P, et al. SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association[J]. PloS one, 2014, 9(6): e99415.

### See Also

`LLSn2List`

### Examples

    ## in this method, we must use disease-gene associations
    ## which genes are represented by entrez ids because of
    ## HumanNet
    data(d2g_fundo_entrezid)
    data(HumanNet_sample)
    ## we specified 5 DOIDs to match Human_sample
    ds<-c("DOID:8176","DOID:2394","DOID:3744","DOID:8466","DOID:5679")
    llsnlist<-LLSn2List(HumanNet_sample)
    FunSim(ds,ds,d2g_fundo_entrezid,llsnlist)

[Package dSimer version 1.8.0 Index]