npGSEA: Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Version 1.12.0

Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.

AuthorJessica Larson and Art Owen
Bioconductor views GeneSetEnrichment Microarray Pathways StatisticalMethod
Date of publicationNone
MaintainerJessica Larson <larson.jess@gmail.com>
LicenseArtistic-2.0
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("npGSEA")

Popular man pages

chiSqStat-methods: ~~ Methods for Function 'chiSqStat' ~~
npGSEAPlot-methods: ~~ Methods for Function 'npGSEAPlot' ~~
npGSEAResultBeta-class: Class '"npGSEAResultBeta"'
npGSEAResultNormCollection-class: Class '"npGSEAResultNormCollection"'
pRight-methods: ~~ Methods for Function 'pRight' ~~
xSet-methods: ~~ Methods for Function 'xSet' ~~
zStat-methods: ~~ Methods for Function 'zStat' ~~
See all...

All man pages Function index File listing

Man pages

alphaValue-methods: ~~ Methods for Function 'alphaValue' ~~
betaHats-methods: ~~ Methods for Function 'betaHats' ~~
betaStat-methods: ~~ Methods for Function 'betaStat' ~~
betaValue-methods: ~~ Methods for Function 'betaValue' ~~
chiSqStat-methods: ~~ Methods for Function 'chiSqStat' ~~
DF-methods: ~~ Methods for Function 'DF' ~~
geneSetName-methods: ~~ Methods for Function 'geneSetName' ~~
getIncidence: Determines the incidence of a gene set in a list of genes.
npGSEA: Calculates an approximation of the permutation GSEA...
npGSEAPlot-methods: ~~ Methods for Function 'npGSEAPlot' ~~
npGSEAResultBeta-class: Class '"npGSEAResultBeta"'
npGSEAResultBetaCollection-class: Class '"npGSEAResultBetaCollection"'
npGSEAResultChiSq-class: Class '"npGSEAResultChiSq"'
npGSEAResultChiSqCollection-class: Class '"npGSEAResultChiSqCollection"'
npGSEAResultNorm-class: Class '"npGSEAResultNorm"'
npGSEAResultNormCollection-class: Class '"npGSEAResultNormCollection"'
pLeft-methods: ~~ Methods for Function 'pLeft' ~~
pRight-methods: ~~ Methods for Function 'pRight' ~~
pTwoSided-methods: ~~ Methods for Function 'pTwoSided' ~~
pValues-methods: ~~ Methods for Function 'pValues' ~~
show-methods: ~~ Methods for Function 'show' in Package 'base' ~~
sigmaSq-methods: ~~ Methods for Function 'sigmaSq' ~~
stat-methods: ~~ Methods for Function 'stat' ~~
xSet-methods: ~~ Methods for Function 'xSet' ~~
zStat-methods: ~~ Methods for Function 'zStat' ~~

Functions

DF Man page
DF,npGSEAResultChiSq-method Man page
DF,npGSEAResultChiSqCollection-method Man page
DF-methods Man page
adjustY Source code
alphaValue Man page
alphaValue,npGSEAResultBeta-method Man page
alphaValue,npGSEAResultBetaCollection-method Man page
alphaValue-methods Man page
betaHats Man page
betaHats,npGSEAResultBeta-method Man page
betaHats,npGSEAResultBetaCollection-method Man page
betaHats,npGSEAResultChiSq-method Man page
betaHats,npGSEAResultChiSqCollection-method Man page
betaHats,npGSEAResultNorm-method Man page
betaHats,npGSEAResultNormCollection-method Man page
betaHats-methods Man page
betaStat Man page
betaStat,npGSEAResultBeta-method Man page
betaStat,npGSEAResultBetaCollection-method Man page
betaStat-methods Man page
betaValue Man page
betaValue,npGSEAResultBeta-method Man page
betaValue,npGSEAResultBetaCollection-method Man page
betaValue-methods Man page
calcBetaHatG Source code
calcChatGw Source code
calcChiSqMoments Source code
calcPvaluesBeta Source code
calcPvaluesNorm Source code
calcThatGw Source code
calcVarThatGw Source code
center Source code
checkxg Source code
chiSqStat Man page
chiSqStat,npGSEAResultChiSq-method Man page
chiSqStat,npGSEAResultChiSqCollection-method Man page
chiSqStat-methods Man page
geneSetName Man page
geneSetName,npGSEAResultBeta-method Man page
geneSetName,npGSEAResultBetaCollection-method Man page
geneSetName,npGSEAResultChiSq-method Man page
geneSetName,npGSEAResultChiSqCollection-method Man page
geneSetName,npGSEAResultNorm-method Man page
geneSetName,npGSEAResultNormCollection-method Man page
geneSetName-methods Man page
getA Source code
getB Source code
getIncidence Man page Source code
getResids Source code
locGenes Source code
npGSEA Man page Source code
npGSEAPlot Man page
npGSEAPlot,npGSEAResultBeta-method Man page
npGSEAPlot,npGSEAResultChiSq-method Man page
npGSEAPlot,npGSEAResultNorm-method Man page
npGSEAPlot-methods Man page
npGSEAResultBeta-class Man page
npGSEAResultBetaCollection-class Man page
npGSEAResultChiSq-class Man page
npGSEAResultChiSqCollection-class Man page
npGSEAResultNorm-class Man page
npGSEAResultNormCollection-class Man page
pLeft Man page
pLeft,npGSEAResultBeta-method Man page
pLeft,npGSEAResultBetaCollection-method Man page
pLeft,npGSEAResultNorm-method Man page
pLeft,npGSEAResultNormCollection-method Man page
pLeft-methods Man page
pRight Man page
pRight,npGSEAResultBeta-method Man page
pRight,npGSEAResultBetaCollection-method Man page
pRight,npGSEAResultNorm-method Man page
pRight,npGSEAResultNormCollection-method Man page
pRight-methods Man page
pTwoSided Man page
pTwoSided,npGSEAResultBeta-method Man page
pTwoSided,npGSEAResultBetaCollection-method Man page
pTwoSided,npGSEAResultChiSq-method Man page
pTwoSided,npGSEAResultChiSqCollection-method Man page
pTwoSided,npGSEAResultNorm-method Man page
pTwoSided,npGSEAResultNormCollection-method Man page
pTwoSided-methods Man page
pValues Man page
pValues,npGSEAResultBeta-method Man page
pValues,npGSEAResultChiSq-method Man page
pValues,npGSEAResultNorm-method Man page
pValues-methods Man page
prepW Source code
prepXYZ Source code
runBetaApprox Source code
runChisqApprox Source code
runNormApprox Source code
show Man page
show,npGSEAResultBeta-method Man page
show,npGSEAResultChiSq-method Man page
show,npGSEAResultNorm-method Man page
show-methods Man page
sigmaSq Man page
sigmaSq,npGSEAResultBeta-method Man page
sigmaSq,npGSEAResultBetaCollection-method Man page
sigmaSq,npGSEAResultChiSq-method Man page
sigmaSq,npGSEAResultChiSqCollection-method Man page
sigmaSq,npGSEAResultNorm-method Man page
sigmaSq,npGSEAResultNormCollection-method Man page
sigmaSq-methods Man page
stat Man page
stat,npGSEAResultBeta-method Man page
stat,npGSEAResultBetaCollection-method Man page
stat,npGSEAResultChiSq-method Man page
stat,npGSEAResultChiSqCollection-method Man page
stat,npGSEAResultNorm-method Man page
stat,npGSEAResultNormCollection-method Man page
stat-methods Man page
xSet Man page
xSet,npGSEAResultBeta-method Man page
xSet,npGSEAResultBetaCollection-method Man page
xSet,npGSEAResultChiSq-method Man page
xSet,npGSEAResultChiSqCollection-method Man page
xSet,npGSEAResultNorm-method Man page
xSet,npGSEAResultNormCollection-method Man page
xSet-methods Man page
zStat Man page
zStat,npGSEAResultNorm-method Man page
zStat,npGSEAResultNormCollection-method Man page
zStat-methods Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/getIncidence.R
R/miscDataPrepFunctions.R
R/miscFunctions.R
R/npGSEA.R
R/npGSEAPlot-methods.R
R/npGSEAResultBeta-accessors.R
R/npGSEAResultChiSq-accessors.R
R/npGSEAResultNorm-accessors.R
R/pValues-methods.R
R/show-methods.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/npGSEA.R
inst/doc/npGSEA.Rnw
inst/doc/npGSEA.pdf
man
man/DF-methods.Rd
man/alphaValue-methods.Rd
man/betaHats-methods.Rd
man/betaStat-methods.Rd
man/betaValue-methods.Rd
man/chiSqStat-methods.Rd
man/geneSetName-methods.Rd
man/getIncidence.Rd
man/npGSEA.Rd
man/npGSEAPlot-methods.Rd
man/npGSEAResultBeta-class.Rd
man/npGSEAResultBetaCollection-class.Rd
man/npGSEAResultChiSq-class.Rd
man/npGSEAResultChiSqCollection-class.Rd
man/npGSEAResultNorm-class.Rd
man/npGSEAResultNormCollection-class.Rd
man/pLeft-methods.Rd
man/pRight-methods.Rd
man/pTwoSided-methods.Rd
man/pValues-methods.Rd
man/show-methods.Rd
man/sigmaSq-methods.Rd
man/stat-methods.Rd
man/xSet-methods.Rd
man/zStat-methods.Rd
vignettes
vignettes/npGSEA.Rnw
npGSEA documentation built on May 20, 2017, 9:16 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.