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Last data update: 2014.03.03

R: Searching for enriched functional modules by pvclust

Arora2010.ModuleSearchByPvclust

R Documentation

Searching for enriched functional modules by pvclust

Description

This function invokes pvclustModule to search for enriched functional gene modules by hierarchical clustering with multiscale bootstrap resampling (using R package pvclust).

Usage

Arora2010.ModuleSearchByPvclust(pan, nboot=1000, metric="cosine2", hclustMethod=
"average", filter=TRUE)

Arguments

`pan`	an object of class `PAN`, in which a posterior association network has already been inferred.
`nboot`	a numeric value giving the number of bootstraps for `pvclust`.
`metric`	a character value specifying which distance metric to use for the hierarchical clustering: 'cosine' (first-order), 'cosine2' (second-order), 'correlation', 'uncentered', 'abscor' or those allowed by the argument 'method' in `dist`.
`hclustMethod`	the agglomerative method used in hierarchical clustering: 'average', 'ward', 'single', 'complete', 'mcquitty', 'median' or 'centroid' (see the argument `method` in `hclust` for more details).
`filter`	a logical value specifying whether or not to filter out screening data of genes without significant associations with all the other genes.

Value

This function will return an object of class PAN with inferred gene modules (modules$clusters) and corresponding p-values (modules$pval) updated in slot 'modules'.

Author(s)

Xin Wang xw264@cam.ac.uk

References

Arora S, Gonzales IM, Hagelstrom RT, et al. (2010). RNAi phenotype profiling of kinases identifies potential therapeutic targets in Ewing's sarcoma. Molecular Cancer, 9(1), 218.

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(pan_Arora2010, package="Mulder2012")
pan_Arora2010<-ModuleSearchByPvclust(pan=pan_Arora2010, nboot=10000, metric=
"cosine2", hclustMethod="average", filter=TRUE)
summarize(pan_Arora2010, what="module")

## End(Not run)