BOG: calculate disease similarity by BOG

In dSimer: Integration of Disease Similarity Methods

Description

given two vectors of diseases and a list of disease-gene associations, this function will calculate disease similarity by method BOG.

Usage

BOG(D1, D2, d2g)

Arguments

D1	a vector consists disease ids
D2	another vector consists disease ids
d2g	a list of disease-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. Automated ontological gene annotation for computing disease similarity[J]. AMIA Summits on Translational Science Proceedings, 2010, 2010: 12

See Also

Normalize

Examples

data(d2g_separation) #get disease-gene associations
ds<-sample(names(d2g_separation),5)
sim<-BOG(ds,ds,d2g_separation)
Normalize(sim) #normalize BOG sim scores

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union



calculating Information Content of diseases..
calculating similarity matrix of diseases.. this may take a while..
normalize the similarity matrix.. this may also take a while..
done..
                           ankylosis pathologic processes
ankylosis                          1         0.0000000000
pathologic processes               0         0.7384994134
abnormalities, multiple            0         0.0026504631
spondylitis, ankylosing            1         0.0000000000
neurodegenerative diseases         0         0.0008794125
                           abnormalities, multiple spondylitis, ankylosing
ankylosis                              0.000000000                       1
pathologic processes                   0.002650463                       0
abnormalities, multiple                0.715169791                       0
spondylitis, ankylosing                0.000000000                       1
neurodegenerative diseases             0.008391091                       0
                           neurodegenerative diseases
ankylosis                                0.0000000000
pathologic processes                     0.0008794125
abnormalities, multiple                  0.0083910908
spondylitis, ankylosing                  0.0000000000
neurodegenerative diseases               0.4830851690

dSimer documentation built on May 2, 2019, 12:40 a.m.