DrugVsDisease-package: DrugVsDisease Package Overview

In DrugVsDisease: Comparison of disease and drug profiles using Gene set Enrichment Analysis

Description

This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express [1] or GEO [2], or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma [3]. Enrichment scores [4] are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Significance scores are output in Cytoscape http://www.cytoscape.org/ format.

Details

Package:	DvD
Type:	Package
Version:	1.0
Date:	2012-06-15
License:	GPL-2
LazyLoad:	yes

Profiles are calculated via generateprofiles and selected profiles are then classified using classifyprofile.

Author(s)

C. Pacini

Maintainer: J Saez-Rodriguez <[e-mail]>

References

[1]Parkinson et al. (2010) ArrayExpress update an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucl. Acids Res.,doi: 10.1093/nar/gkq1040.

[2]Barrett T et al. (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucl. Acids Res, 39, D1005-D1010.

[3]Smyth et al. (2004). Linear models and empirical Bayes method for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3.

[4]Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.

See Also

generateprofiles, selectrankedlists, classifyprofile

Examples

#profileAE<-generateprofiles(input="AE",accession="E-GEOD-22528")
#selprofiles<-selectrankedlists(profileAE,1)
#default<-classifyprofile(data=selprofiles$ranklist, signif.fdr=1.1)

DrugVsDisease documentation built on Nov. 8, 2020, 5:56 p.m.