ICMg - Interaction component models for gene modules

Description

Probabilistic analysis of protein-protein interaction measurements and gene expression data. Provides functions for computing component membership distributions for genes, also interpretable as functional gene modules or clusters.

Details

Package:	ICMg
Type:	Package
Version:	1.0
Date:	2009-03-09
License:	GNU GPL 3 or any later version (at your option)

Function ICMg.combined.sampler can be used to sample components for combined interaction and functional data. ICMg.links.sampler does the same for interaction data only. There are two versions of the iteration functions available (R and C) and it is highly recommended to use the faster C versions.

Author(s)

Juuso Parkkinen <juuso.parkkinen@tkk.fi> Maintainer: Juuso Parkkinen <juuso.parkkinen@tkk.fi>

References

TBA

Examples

        ## Load data and set parameters
        data(osmo)
        C.boost = 1 ## Use faster C funtions
        alpha = 10
        beta = 0.01
        B.num = 2
        B.size = 5
        S.num = 2  
        S.size = 5
        C = 10
        pm0 = 0
        V0 = 1               
        V = 0.1

        ## Run sampling
        res = ICMg.combined.sampler(osmo$ppi, osmo$exp, C, alpha, beta, pm0, V0, V, B.num, B.size, S.num, S.size, C.boost) 
        ## Compute component membership probabilities for nodes
        res$comp.memb <- ICMg.get.comp.memberships(osmo$ppi, res)
        ## Compute (hard) clustering for nodes
        res$clustering <- apply(res$comp.memb, 2, which.max)