edge: Extraction of Differential Gene Expression

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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.

Author
John D. Storey, Jeffrey T. Leek and Andrew J. Bass
Date of publication
None
Maintainer
John D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@princeton.edu>
License
MIT + file LICENSE
Version
2.6.0
URLs

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

Files in this package

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