FunSim: calculate disease similarity by FunSim
In PengNi/dSimer: Integration of Disease Similarity Methods

Description Usage Arguments Value Author(s) References See Also Examples

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

1	FunSim(D1, D2, d2g, LLSnList)

`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

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

Peng Ni, Min Li

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.

LLSn2List

## 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)