modulediscoverer: Module Discoverer
In ddeweerd/MODifieRDev: MODifieRDev

Description Usage Arguments Details Value References See Also

A clique based algorithm by Vlaic et al. to produce disease module from Differentially Expressed Genes

1
2
3

modulediscoverer(MODifieR_input, ppi_network, permutations = 10000,
  deg_cutoff = 0.05, repeats = 15, clique_cutoff = 0.01,
  dataset_name = NULL)

`MODifieR_input`	A MODifieR input object produced by one of the `create_input` functions
`ppi_network`	A network as a dataframe where the first 2 columns are the interactions
`permutations`	Number of permutations to perform to identify the community structure
`deg_cutoff`	p-value cutoff for differentialy expressed genes
`repeats`	Number of times the algorithm is repeated
`clique_cutoff`	cutoff pvalue for significant cliques
`dataset_name`	Optional name for the input object that will be stored in the settings object. Default is the variable name of the input object

This is an implementation of the single seed Module Discoverer algorithm. The code has been adapted from the orignal code by Vlaic et al. For details, please see the paper referenced below

modulediscoverer returns an object of class "MODifieR_module" with subclass "module_discoverer". This object is a named list containing the following components:

`module_genes`	A character vector containing the genes in the final module
`graph`	`igraph` graph containing the disease module
`settings`	A named list containing the parameters used in generating the object

Vlaic, S., Tokarski-schnelle, C., Gustafsson, M., Dahmen, U., Guthke, R., & Schuster, S. (2017). ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks., 1–17.

https://www.leibniz-hki.de/en/modulediscoverer.html

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