FunSim {dSimer} | R Documentation |
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
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.
## 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)