A pipeline to do network analyses in Wang et al 2012 for Arora S et al 2010

Description

This pipeline function reproducing results in Wang X et al., 2012 for RNAi screening data of Ewing's sarcoma in Arora S et al., 2010.

Usage

Arora2010.pipeline(par4BM=list(model="global", metric="cosine", nPerm=20),
par4PAN=list(type="SNR", log=TRUE, sign=TRUE, cutoff=log(10), filter=FALSE),
par4ModuleSearch=list(nboot=10000, metric="cosine2", hclustMethod="average", 
filter=FALSE))

Arguments

Details

This function reproduces results of network inference in Wang X et al., 2012 for RNAi screening data of Ewing's sarcoma in Arora S et al., 2010.:

(1) Beta-mixture modelling of functional gene associations (see Arora2010.BMfitting)) for details.

(2) Inferring a posterior association network (see Arora2010.InferPAN)) for details.

(3) Searching enriched gene modules by pvclust (see Arora2010.ModuleSearchByPvclust)) for details.

(4) Pathway analyses (see Arora2010.hypergeo)) for details.

Value

All results will be saved in the current work directory.

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.

See Also

Arora2010.BMfitting, Arora2010.InferPAN, Arora2010.ModuleSearchByPvclust, Arora2010.hypergeo

Examples

## Not run: 
Arora2010.pipeline()

## End(Not run)

Results