Permutation approximation methods for gene set enrichment
analysis (non-permutation GSEA)
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Documentation for package ‘npGSEA’ version 1.43.0
Help Pages
| 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' ~~ |