Separation: calculating network-based separation of disease pairs
In dSimer: Integration of Disease Similarity Methods

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

given two vectors of diseases, a list of disease-gene associations and a PPI network, this function will calculate network-based separation by method Separation.

1	Separation(D1, D2, d2g, graph)

`D1`	a vector consists disease ids
`D2`	another vector consists disease ids
`d2g`	a list of disease-gene associations
`graph`	an igraph graph object of PPI network

a matrix of disease disease network-based separation which rownames is D1 and colnames is D2

Peng Ni, Min Li

Menche J, Sharma A, Kitsak M, et al. Uncovering disease-disease relationships through the incomplete interactome[J]. Science, 2015, 347(6224): 1257601.

Separation2Similarity

data(d2g_separation)
data(interactome)

graph_interactome<-graph.data.frame(interactome,directed=FALSE)
ds<-sample(names(d2g_separation),5)
sep<-Separation(ds,ds,d2g_separation,graph_interactome)
sim<-Separation2Similarity(sep)
sim

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



filtering disease-gene associations..
calculating separation distance between diseases.. this may need a lot of time.. be patient..
done..
                                colitis limb deformities, congenital
colitis                      0.95209276                   0.12645327
limb deformities, congenital 0.12645327                   1.00000000
thoracic neoplasms           0.10247899                   0.11409347
connective tissue diseases   0.08132086                   0.00000000
movement disorders           0.14617886                   0.08809145
                             thoracic neoplasms connective tissue diseases
colitis                              0.10247899                 0.08132086
limb deformities, congenital         0.11409347                 0.00000000
thoracic neoplasms                   0.93974458                 0.08825901
connective tissue diseases           0.08825901                 0.78475591
movement disorders                   0.09698488                 0.05491106
                             movement disorders
colitis                              0.14617886
limb deformities, congenital         0.08809145
thoracic neoplasms                   0.09698488
connective tissue diseases           0.05491106
movement disorders                   0.91436974