S2B: S2B

In ddeweerd/MODifieRDev: MODifieRDev

Description

Combine two different disease modules into using Specific Betweenness (S2B)

Usage

S2B(MODifieR_module1, MODifieR_module2, ppi_network, nrep = 100,
  nrep2 = 100, n_cores = 4)

Arguments

MODifieR_module1	A MODifieR module inferred by a disease module inference method
MODifieR_module2	A MODifieR module inferred by a disease module inference method
ppi_network	A network as a dataframe where the first 2 columns are the interactions
nrep	number of randomizations (shuffle edges maintaining node degree) to compute specificity score 1
nrep2	number of randomizations (shuffle seed identity) to compute specificity score 2
n_cores	Number of cores to use

Details

S2B prioritizes genes frequently and specifically present in shortest paths linking two disease modules. For a detailed description of the algorithm, see the paper referenced below

Value

Returns an object of class "MODifieR_module" with subclass "S2B". This object is a named list containing the following components:

module_genes	A character vector containing the genes in the final module
input1_class	Method that was used to create disease module 1 (inferred by its class)
input2_class	Method that was used to create disease module 2 (inferred by its class)
settings	A named list containing the parameters used in generating the object

References

Garcia-Vaquero, M. L., Gama-Carvalho, M., Rivas, J. D. Las, & Pinto, F. R. (2018). Searching the overlap between network modules with specific betweeness (S2B) and its application to cross-disease analysis. Scientific Reports, 8(1), 1–10. https://doi.org/10.1038/s41598-018-29990-7

ddeweerd/MODifieRDev documentation built on Nov. 12, 2019, 7:50 a.m.