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

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.

Author
Jessica Larson and Art Owen
Date of publication
None
Maintainer
Jessica Larson <larson.jess@gmail.com>
License
Artistic-2.0
Version
1.10.0

View on Bioconductor

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' ~~

Files in this package

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