PSB {dSimer} | R Documentation |
given two vectors of diseases, a list of disease-GO term associations and a list of GO term-gene associations, this function will calculate disease similarity by method PSB
PSB(D1, D2, d2go, go2g)
D1 |
a vector consists disease ids |
D2 |
another vector consists disease ids |
d2go |
a list of disease-go associations |
go2g |
a list of go-gene associations |
a matrix of disease disease simialrity which rownames is D1 and colnames is D2
Peng Ni, Min Li
Mathur S, Dinakarpandian D. Finding disease similarity based on implicit semantic similarity[J]. Journal of biomedical informatics, 2012, 45(2): 363-371.
get_GOterm2GeneAssos
, HypergeometricTest
,
Normalize
## these are samples of GO-gene associations and disease-GO associations data(go2g_sample) data(d2go_sample) ##### the entire associations can be obtained by follows: ## go2g<-get_GOterm2GeneAssos(GOONTOLOGY = "BP", geneid="SYMBOL") #get go-gene associations ## data(d2g_fundo_symbol) ## d2go<-HypergeometricTest(d2g = d2g_fundo_symbol,go2g = go2g) ##### ################################################### ds<-names(d2go_sample) sim<-PSB(ds,ds,d2go_sample,go2g_sample) Normalize(sim)