Separation: calculating network-based separation of disease pairs

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

View source: R/Separation.R

Description

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.

Usage

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Separation(D1, D2, d2g, graph)

Arguments

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

Value

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

Author(s)

Peng Ni, Min Li

References

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

See Also

Separation2Similarity

Examples

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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

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