edge: Extraction of Differential Gene Expression
Version 2.8.0

The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as snm, sva, and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.

AuthorJohn D. Storey, Jeffrey T. Leek and Andrew J. Bass
Bioconductor views DataImport DifferentialExpression GeneExpression MultipleComparison Regression TimeCourse
Date of publicationNone
MaintainerJohn D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@princeton.edu>
LicenseMIT + file LICENSE
Version2.8.0
URL https://github.com/jdstorey/edge
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("edge")

Getting started

README.md

Popular man pages

build_models: Generate a deSet object with full and null models
deFit-class: The differential expression class for the model fits
edge: Extraction of Differential Gene Expression
individual: Individuals sampled in experiment
kidney: Gene expression dataset from Rodwell et al. (2004)
kl_clust: Modular optimal discovery procedure (mODP)
nullModel: Null model equation from deSet object
See all...

All man pages Function index File listing

Man pages

apply_jackstraw: Non-Parametric Jackstraw for Principal Component Analysis...
apply_qvalue: Estimate the q-values for a given set of p-values
apply_snm: Supervised normalization of data in edge
apply_sva: Estimate surrogate variables
betaCoef: Regression coefficients from full model fit
build_models: Generate a deSet object with full and null models
build_study: Formulates the experimental models
deFit-class: The differential expression class for the model fits
deSet: Create a deSet object from an ExpressionSet
deSet-class: The differential expression class (deSet)
edge: Extraction of Differential Gene Expression
endotoxin: Gene expression dataset from Calvano et al. (2005) Nature
fitFull: Fitted data from the full model
fit_models: Linear regression of the null and full models
fitNull: Fitted data from the null model
fullMatrix: Matrix representation of full model
fullModel: Full model equation
gibson: Gene expression dataset from Idaghdour et al. (2008)
individual: Individuals sampled in experiment
kidney: Gene expression dataset from Rodwell et al. (2004)
kl_clust: Modular optimal discovery procedure (mODP)
lrt: Performs F-test (likelihood ratio test using Normal...
nullMatrix: Matrix representation of null model
nullModel: Null model equation from deSet object
odp: The optimal discovery procedure
qvalueObj: Access/set qvalue slot
resFull: Residuals of full model fit
resNull: Residuals of null model fit
show: Show function for deFit and deSet
sType: Statistic type used in analysis
summary: Summary of deFit and deSet

Functions

apply_jackstraw Man page
apply_jackstraw,deSet-method Man page
apply_qvalue Man page
apply_qvalue,deSet-method Man page
apply_snm Man page
apply_snm,deSet-method Man page
apply_sva Man page
apply_sva,deSet-method Man page
betaCoef Man page
betaCoef,deFit-method Man page
bootstrap Source code
build_models Man page Source code
build_study Man page Source code
createSet Source code
deFit-class Man page
deFitCheck Source code
deSet Man page
deSet,ExpressionSet-method Man page
deSet-class Man page
deSetCheck Source code
edge Man page
edge-package Man page
endotoxin Man page
fitFDist Source code
fitFull Man page
fitFull,deFit-method Man page
fitNull Man page
fitNull,deFit-method Man page
fit_models Man page
fit_models,deSet-method Man page
fit_wmodels Source code
fullMatrix Man page
fullMatrix,deSet-method Man page
fullMatrix<- Man page
fullMatrix<-,deSet-method Man page
fullModel Man page
fullModel,deSet-method Man page
fullModel<- Man page
fullModel<-,deSet-method Man page
gibson Man page
individual Man page
individual,deSet-method Man page
individual<- Man page
individual<-,deSet-method Man page
kidney Man page
kl Source code
kl_clust Man page
kl_clust,deSet,deFit-method Man page
kl_clust,deSet,missing-method Man page
klmod Source code
lrt Man page
lrt,deSet,deFit-method Man page
lrt,deSet,missing-method Man page
lrtStat Source code
mod.df Source code Source code
mod.parms Source code
null Source code
nullMatrix Man page
nullMatrix,deSet-method Man page
nullMatrix<- Man page
nullMatrix<-,deSet-method Man page
nullModel Man page
nullModel,deSet-method Man page
nullModel<- Man page
nullModel<-,deSet-method Man page
odp Man page
odp,deSet,deFit-method Man page
odp,deSet,missing-method Man page
odp.score Source code
odpStat Source code
projMatrix Source code
qvalueObj Man page
qvalueObj,deSet-method Man page
qvalueObj<- Man page
qvalueObj<-,deSet-method Man page
resFull Man page
resFull,deFit-method Man page
resNull Man page
resNull,deFit-method Man page
rescale Source code
rm.zero.cols Source code
sType Man page
sType,deFit-method Man page
show Man page
show,deFit-method Man page
show,deSet-method Man page
squeezeVar Source code
summary Man page
summary,deFit-method Man page
summary,deSet-method Man page
trigammaInverse Source code
updateOldExpSet Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/ExpressionSet-methods.R
R/deFit-methods.R
R/deSet-methods.R
R/edge.R
R/form_models.R
R/getMethods.R
R/kl_clust-functions.R
R/lrt-functions.R
R/misc.R
R/odp-functions.R
R/setMethods.R
R/wls.R
README.md
build
build/vignette.rds
data
data/endotoxin.rda
data/gibson.rda
data/kidney.rda
inst
inst/NEWS
inst/doc
inst/doc/edge.R
inst/doc/edge.Rnw
inst/doc/edge.pdf
man
man/apply_jackstraw.Rd
man/apply_qvalue.Rd
man/apply_snm.Rd
man/apply_sva.Rd
man/betaCoef.Rd
man/build_models.Rd
man/build_study.Rd
man/deFit-class.Rd
man/deSet-class.Rd
man/deSet.Rd
man/edge.Rd
man/endotoxin.Rd
man/fitFull.Rd
man/fitNull.Rd
man/fit_models.Rd
man/fullMatrix.Rd
man/fullModel.Rd
man/gibson.Rd
man/individual.Rd
man/kidney.Rd
man/kl_clust.Rd
man/lrt.Rd
man/nullMatrix.Rd
man/nullModel.Rd
man/odp.Rd
man/qvalueObj.Rd
man/resFull.Rd
man/resNull.Rd
man/sType.Rd
man/show.Rd
man/summary.Rd
src
src/edge-init.c
src/edgeKLODP.c
src/edgeKLODP.h
tests
tests/testthat
tests/testthat.R
tests/testthat/test-edgeSet.R
tests/testthat/test-modelCreation.R
vignettes
vignettes/edge.Rnw
vignettes/edgecomp.pdf
vignettes/edgerefs.bib
edge documentation built on May 20, 2017, 10:23 p.m.