DrugVsDisease Package Overview

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

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

Author(s)

C. Pacini

Maintainer: J Saez-Rodriguez <saezrodriguez@ebi.ac.uk>

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

profiles<-generateprofiles(input="GEO",accession="GDS2617",case="disease",statistic="t",annotation="hgu133a")
selprofile<-selectrankedlists(profiles,6)
classification<-classifyprofile(data=selprofile$ranklist,signif.fdr=1,noperm=20)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DrugVsDisease)
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data

Attaching package: 'cMap2data'

The following object is masked from 'package:DrugVsDiseasedata':

    genelist

Loading required package: qvalue
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DrugVsDisease/DrugVsDisease-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DrugVsDisease-package
> ### Title: DrugVsDisease Package Overview
> ### Aliases: DrugVsDisease-package DrugVsDisease
> ### Keywords: package
> 
> ### ** Examples
> 
> profiles<-generateprofiles(input="GEO",accession="GDS2617",case="disease",statistic="t",annotation="hgu133a")
File stored at: 
./GDS2617.soft.gz
File stored at: 
/tmp/RtmpCBhBel/GPL96.annot.gz
Note: Ensembl genes do not match genelist in reference data. Consider uploading pre-processed lists to classifyprofiles
[1] "Fitted linear models: "
[1] "factornon.tumorigenic.cancer.cell-factornormal:all"                 
[2] "factornon.tumorigenic.cancer.cell-factortumorigenic.cancer.cell:all"
[3] "factornormal-factortumorigenic.cancer.cell:all"                     
[4] "factornormal-factornon.tumorigenic.cancer.cell:all"                 
[5] "factortumorigenic.cancer.cell-factornon.tumorigenic.cancer.cell:all"
[6] "factortumorigenic.cancer.cell-factornormal:all"                     
There were 32 warnings (use warnings() to see them)
> selprofile<-selectrankedlists(profiles,6)
> classification<-classifyprofile(data=selprofile$ranklist,signif.fdr=1,noperm=20)
Number of Significant results greater than 10 Using top 10 hits - consider using average linkage instead
> 
> 
> 
> 
> dev.off()
null device 
          1 
>