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.

AuthorJessica Larson and Art Owen
Date of publicationNone
MaintainerJessica Larson <larson.jess@gmail.com>
LicenseArtistic-2.0
Version1.10.0

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Functions

alphaValue Man page
alphaValue-methods Man page
alphaValue,npGSEAResultBetaCollection-method Man page
alphaValue,npGSEAResultBeta-method Man page
betaHats Man page
betaHats-methods Man page
betaHats,npGSEAResultBetaCollection-method Man page
betaHats,npGSEAResultBeta-method Man page
betaHats,npGSEAResultChiSqCollection-method Man page
betaHats,npGSEAResultChiSq-method Man page
betaHats,npGSEAResultNormCollection-method Man page
betaHats,npGSEAResultNorm-method Man page
betaStat Man page
betaStat-methods Man page
betaStat,npGSEAResultBetaCollection-method Man page
betaStat,npGSEAResultBeta-method Man page
betaValue Man page
betaValue-methods Man page
betaValue,npGSEAResultBetaCollection-method Man page
betaValue,npGSEAResultBeta-method Man page
chiSqStat Man page
chiSqStat-methods Man page
chiSqStat,npGSEAResultChiSqCollection-method Man page
chiSqStat,npGSEAResultChiSq-method Man page
DF Man page
DF-methods Man page
DF,npGSEAResultChiSqCollection-method Man page
DF,npGSEAResultChiSq-method Man page
geneSetName Man page
geneSetName-methods Man page
geneSetName,npGSEAResultBetaCollection-method Man page
geneSetName,npGSEAResultBeta-method Man page
geneSetName,npGSEAResultChiSqCollection-method Man page
geneSetName,npGSEAResultChiSq-method Man page
geneSetName,npGSEAResultNormCollection-method Man page
geneSetName,npGSEAResultNorm-method Man page
getIncidence Man page
npGSEA Man page
npGSEAPlot Man page
npGSEAPlot-methods Man page
npGSEAPlot,npGSEAResultBeta-method Man page
npGSEAPlot,npGSEAResultChiSq-method Man page
npGSEAPlot,npGSEAResultNorm-method 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-methods Man page
pLeft,npGSEAResultBetaCollection-method Man page
pLeft,npGSEAResultBeta-method Man page
pLeft,npGSEAResultNormCollection-method Man page
pLeft,npGSEAResultNorm-method Man page
pRight Man page
pRight-methods Man page
pRight,npGSEAResultBetaCollection-method Man page
pRight,npGSEAResultBeta-method Man page
pRight,npGSEAResultNormCollection-method Man page
pRight,npGSEAResultNorm-method Man page
pTwoSided Man page
pTwoSided-methods Man page
pTwoSided,npGSEAResultBetaCollection-method Man page
pTwoSided,npGSEAResultBeta-method Man page
pTwoSided,npGSEAResultChiSqCollection-method Man page
pTwoSided,npGSEAResultChiSq-method Man page
pTwoSided,npGSEAResultNormCollection-method Man page
pTwoSided,npGSEAResultNorm-method Man page
pValues Man page
pValues-methods Man page
pValues,npGSEAResultBeta-method Man page
pValues,npGSEAResultChiSq-method Man page
pValues,npGSEAResultNorm-method Man page
show Man page
show-methods Man page
show,npGSEAResultBeta-method Man page
show,npGSEAResultChiSq-method Man page
show,npGSEAResultNorm-method Man page
sigmaSq Man page
sigmaSq-methods Man page
sigmaSq,npGSEAResultBetaCollection-method Man page
sigmaSq,npGSEAResultBeta-method Man page
sigmaSq,npGSEAResultChiSqCollection-method Man page
sigmaSq,npGSEAResultChiSq-method Man page
sigmaSq,npGSEAResultNormCollection-method Man page
sigmaSq,npGSEAResultNorm-method Man page
stat Man page
stat-methods Man page
stat,npGSEAResultBetaCollection-method Man page
stat,npGSEAResultBeta-method Man page
stat,npGSEAResultChiSqCollection-method Man page
stat,npGSEAResultChiSq-method Man page
stat,npGSEAResultNormCollection-method Man page
stat,npGSEAResultNorm-method Man page
xSet Man page
xSet-methods Man page
xSet,npGSEAResultBetaCollection-method Man page
xSet,npGSEAResultBeta-method Man page
xSet,npGSEAResultChiSqCollection-method Man page
xSet,npGSEAResultChiSq-method Man page
xSet,npGSEAResultNormCollection-method Man page
xSet,npGSEAResultNorm-method Man page
zStat Man page
zStat-methods Man page
zStat,npGSEAResultNormCollection-method Man page
zStat,npGSEAResultNorm-method Man page

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