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Last data update: 2014.03.03

R: Plot a figure illustrating enrichment analysis results

GSEARandomWalkFig

R Documentation

Plot a figure illustrating enrichment analysis results

Description

The function invokes functions in R package HTSanalyzeR to plot results of enrichment analysis of functional interactions for protein-protein interactions.

Usage

GSEARandomWalkFig(pheno, PPI, bm, what="pos")

Arguments

`pheno`	a numeric matrix of z-scores with rows and columns corresponding to samples and genes, respectively.
`PPI`	an adjacency matrix of protein-protein interactions extracted from the PINdb (details in `Mulder2012.PPIPre`).
`bm`	an object of S4 class `BetaMixture`, which models functional interactions between genes (see `BetaMixture`).
`what`	a character value specifying which component should be plotted: ‘pos’ (positive association), ‘neg’ (negative association) or ‘none’ (lack of association).

Author(s)

Xin Wang xw264@cam.ac.uk

References

Mulder KW, Wang X, Escriu C, et al. (2012). Diverse epigenetic strategies interact to control epidermal differentiation. Nature Cell Biology. doi:10.1038/ncb2520.

Wang X, Castro MA, Mulder KW and Markowetz F (2012), Posterior association networks and enriched functional gene modules inferred from rich phenotypic perturbation screens, PLoS Computational Biology, doi:10.1371/journal.pcbi.1002566.

Examples

## Not run: 
data(Mulder2012, package="Mulder2012")
data(Mulder2012.PPI, package="Mulder2012")
data(bm_Mulder2012, package="Mulder2012")
GSEARandomWalkFig(Mulder2012, PPI, bm_Mulder2012, what="pos")

## End(Not run)