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Last data update: 2014.03.03

R: Infer a posterior association network given a fitted...

Arora2010.InferPAN

R Documentation

Infer a posterior association network given a fitted BetaMixture object

Description

The function infers a functional association network given an object of class BetaMixture that has been fitted.

Usage

Arora2010.InferPAN(bm, type="SNR", log=TRUE, sign=TRUE, cutoff=log(10), 
filter=FALSE)

Arguments

`bm`	an object of S4 class `BetaMixture`, which models the densities of first-order similarities between genes (see `BetaMixture`).
`type`	a character value giving the type of edge weights: signal-to-noise ratio ('SNR'), posterior probability ratio ('PPR') or posterior probability ('PP')
`log`	a logical value specifying whether or not to compute logrithms for edge weights.
`sign`	a logical value specifying whether a signed graph should be inferred. It is only used when `type='SNR'`.
`cutoff`	a numeric value giving the threshold to tell the significance of an edge.
`filter`	a logical value specifying whether or not to filter out genes without any significant association with all the other genes.

Details

This function first initiates an object of class PAN with bm, which is an object of class BetaMixture that is supposed to have been fitted. The function infer is then invoked to infer a posterior association network given the inputted arguments type, log, sign, cutoff and filter.

Value

an object of class PAN with the inferred posterior association network stored at slot graph

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(bm_Arora2010, package="Mulder2012")
Arora2010.InferPAN(bm=bm_Arora2010, type="SNR", log=TRUE, sign=TRUE, cutoff=
log(10), filter=FALSE) 

## End(Not run)