FunSim: calculate disease similarity by FunSim

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

View source: R/SemFunSim.R

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

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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

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## 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)

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