PSB: calculate disease similarity by PSB

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

View source: R/PSB.R

Description

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

Usage

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PSB(D1, D2, d2go, go2g)

Arguments

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

Value

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

Author(s)

Peng Ni, Min Li

References

Mathur S, Dinakarpandian D. Finding disease similarity based on implicit semantic similarity[J]. Journal of biomedical informatics, 2012, 45(2): 363-371.

See Also

get_GOterm2GeneAssos, HypergeometricTest, Normalize

Examples

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## 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)

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