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


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Documentation for package ‘npGSEA’ version 1.43.0

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alphaValue ~~ Methods for Function 'alphaValue' ~~
alphaValue-method ~~ Methods for Function 'alphaValue' ~~
alphaValue-methods ~~ Methods for Function 'alphaValue' ~~
betaHats ~~ Methods for Function 'betaHats' ~~
betaHats-method ~~ Methods for Function 'betaHats' ~~
betaHats-methods ~~ Methods for Function 'betaHats' ~~
betaStat ~~ Methods for Function 'betaStat' ~~
betaStat-method ~~ Methods for Function 'betaStat' ~~
betaStat-methods ~~ Methods for Function 'betaStat' ~~
betaValue ~~ Methods for Function 'betaValue' ~~
betaValue-method ~~ Methods for Function 'betaValue' ~~
betaValue-methods ~~ Methods for Function 'betaValue' ~~
chiSqStat ~~ Methods for Function 'chiSqStat' ~~
chiSqStat-method ~~ Methods for Function 'chiSqStat' ~~
chiSqStat-methods ~~ Methods for Function 'chiSqStat' ~~
DF ~~ Methods for Function 'DF' ~~
DF-method ~~ Methods for Function 'DF' ~~
DF-methods ~~ Methods for Function 'DF' ~~
geneSetName ~~ Methods for Function 'geneSetName' ~~
geneSetName-method ~~ Methods for Function 'geneSetName' ~~
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 statistics and p-values
npGSEAPlot ~~ Methods for Function 'npGSEAPlot' ~~
npGSEAPlot-method ~~ Methods for Function 'npGSEAPlot' ~~
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 for Function 'pLeft' ~~
pLeft-method ~~ Methods for Function 'pLeft' ~~
pLeft-methods ~~ Methods for Function 'pLeft' ~~
pRight ~~ Methods for Function 'pRight' ~~
pRight-method ~~ Methods for Function 'pRight' ~~
pRight-methods ~~ Methods for Function 'pRight' ~~
pTwoSided ~~ Methods for Function 'pTwoSided' ~~
pTwoSided-method ~~ Methods for Function 'pTwoSided' ~~
pTwoSided-methods ~~ Methods for Function 'pTwoSided' ~~
pValues ~~ Methods for Function 'pValues' ~~
pValues-method ~~ Methods for Function 'pValues' ~~
pValues-methods ~~ Methods for Function 'pValues' ~~
show ~~ Methods for Function 'show' in Package 'base' ~~
show-method ~~ Methods for Function 'show' in Package 'base' ~~
show-methods ~~ Methods for Function 'show' in Package 'base' ~~
sigmaSq ~~ Methods for Function 'sigmaSq' ~~
sigmaSq-method ~~ Methods for Function 'sigmaSq' ~~
sigmaSq-methods ~~ Methods for Function 'sigmaSq' ~~
stat ~~ Methods for Function 'stat' ~~
stat-method ~~ Methods for Function 'stat' ~~
stat-methods ~~ Methods for Function 'stat' ~~
xSet ~~ Methods for Function 'xSet' ~~
xSet-method ~~ Methods for Function 'xSet' ~~
xSet-methods ~~ Methods for Function 'xSet' ~~
zStat ~~ Methods for Function 'zStat' ~~
zStat-method ~~ Methods for Function 'zStat' ~~
zStat-methods ~~ Methods for Function 'zStat' ~~