edge: Extraction of Differential Gene Expression

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
Date of publicationNone
MaintainerJohn D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@princeton.edu>
LicenseMIT + file LICENSE
Version2.6.0
https://github.com/jdstorey/edge

View on Bioconductor

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
build_models Man page
build_study Man page
deFit-class Man page
deSet Man page
deSet-class Man page
deSet,ExpressionSet-method Man page
edge Man page
edge-package Man page
endotoxin Man page
fitFull Man page
fitFull,deFit-method Man page
fit_models Man page
fit_models,deSet-method Man page
fitNull Man page
fitNull,deFit-method Man page
fullMatrix Man page
fullMatrix<- Man page
fullMatrix<-,deSet-method Man page
fullMatrix,deSet-method Man page
fullModel Man page
fullModel<- Man page
fullModel<-,deSet-method Man page
fullModel,deSet-method Man page
gibson Man page
individual Man page
individual<- Man page
individual<-,deSet-method Man page
individual,deSet-method Man page
kidney Man page
kl_clust Man page
kl_clust,deSet,deFit-method Man page
kl_clust,deSet,missing-method Man page
lrt Man page
lrt,deSet,deFit-method Man page
lrt,deSet,missing-method Man page
nullMatrix Man page
nullMatrix<- Man page
nullMatrix<-,deSet-method Man page
nullMatrix,deSet-method Man page
nullModel Man page
nullModel<- Man page
nullModel<-,deSet-method Man page
nullModel,deSet-method Man page
odp Man page
odp,deSet,deFit-method Man page
odp,deSet,missing-method Man page
qvalueObj Man page
qvalueObj<- Man page
qvalueObj<-,deSet-method Man page
qvalueObj,deSet-method Man page
resFull Man page
resFull,deFit-method Man page
resNull Man page
resNull,deFit-method Man page
show Man page
show,deFit-method Man page
show,deSet-method Man page
sType Man page
sType,deFit-method Man page
summary Man page
summary,deFit-method Man page
summary,deSet-method Man page

Files

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

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