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

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

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