mod_mcode: MCODE
In ddeweerd/MODifieRDev: MODifieRDev

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

A clique based algorithm to identify disease modules from differentially expressed genes originally by Bader et al

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mod_mcode(MODifieR_input, ppi_network, hierarchy = 1, vwp = 0.5,
  haircut = F, fluff = F, fdt = 0.8, loops = T,
  deg_cutoff = 0.05, module_cutoff = 3.5, 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
`hierarchy`	This parameter indicates how many hierarchy are included in the network, currently it can be `0`, `1` or `2`. Default value is `1`.
`vwp`	Vertex weight percentage. Default value is 0.5.
`haircut`	Boolean value, whether to remove singly-connected nodes from clusters (TRUE) or not (FALSE).
`fluff`	Boolean value, whether to spand cluster cores by one neighbour shell outwards (TRUE) or not (FALSE).
`fdt`	Cluster density cutoff. Default value is 0.8.
`loops`	Boolean value, whether to include self-loops (TRUE) or not (FALSE).
`deg_cutoff`	p-value cutoff for differentialy expressed genes
`module_cutoff`	Minimal score for a module to be returned
`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

Much of the code an documentation has been taken from the now defunct package "ProNet"

mcode returns a list of objects of class "MODifieR_module" with subclass "Mcode". The objects are named lists containing the following components:

`module_genes`	A character vector containing the genes in the final module
`module_scores`	A numeric value that denotes the score of the module. Higher is better
`settings`	A named list containing the parameters used in generating the object

DIrk de Weerd

Bader, G. D., & Hogue, C. W. (2003). An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4(1), 2. https://doi.org/10.1186/1471-2105-4-2

https://github.com/cran/ProNet

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