PSB {dSimer} | R Documentation

## calculate disease similarity by PSB

### 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

    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

    ## 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)

[Package dSimer version 1.12.0 Index]