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| GeneSelector-package | Stability and aggregation of ranked gene lists |
| AdjustPvalues | Internal functions |
| AggregatedRanking | "AggregatedRanking" |
| AggregatedRanking-class | "AggregatedRanking" |
| AggregateMC | Aggregation of repeated rankings using a Markov chain approach |
| AggregateMC-method | Aggregation of repeated rankings using a Markov chain approach |
| AggregateMC-methods | Aggregation of repeated rankings using a Markov chain approach |
| AggregatePenalty | Aggregation of repeated rankings using a variance penalty approach |
| AggregatePenalty-method | Aggregation of repeated rankings using a variance penalty approach |
| AggregatePenalty-methods | Aggregation of repeated rankings using a variance penalty approach |
| AggregateSimple | Simple aggregation of repeated rankings |
| AggregateSimple-method | Simple aggregation of repeated rankings |
| AggregateSimple-methods | Simple aggregation of repeated rankings |
| AggregateSVD | Agregation of repeated rankings using the singular value decomposition (SVD) |
| AggregateSVD-method | Agregation of repeated rankings using the singular value decomposition (SVD) |
| AggregateSVD-methods | Agregation of repeated rankings using the singular value decomposition (SVD) |
| BootMatrix | "BootMatrix" |
| BootMatrix-class | "BootMatrix" |
| combn | Internal functions |
| dispersion | Compute genewise dispersion measures for repeated rankings |
| dispersion-method | Compute genewise dispersion measures for repeated rankings |
| FoldMatrix | "FoldMatrix" |
| FoldMatrix-class | "FoldMatrix" |
| FoldMatrix-method | "FoldMatrix" |
| GeneRanking | "GeneRanking" |
| GeneRanking-class | "GeneRanking" |
| GenerateBootMatrix | Altered datasets via bootstrap |
| GenerateBootMatrix-method | Altered datasets via bootstrap |
| GenerateBootMatrix-methods | Altered datasets via bootstrap |
| GenerateFoldMatrix | Altered datasets via k-Jackknife or label exchange |
| GenerateFoldMatrix-method | Altered datasets via k-Jackknife or label exchange |
| GenerateFoldMatrix-methods | Altered datasets via k-Jackknife or label exchange |
| GeneSelector | Select promising candidate genes |
| GeneSelector-method | Select promising candidate genes |
| GeneSelector-methods | Select promising candidate genes |
| GeneSelectorOutput | "GeneSelectorOutputRanking" |
| GeneSelectorOutput-class | "GeneSelectorOutputRanking" |
| getLambda | Internal functions |
| GetStabilityDistance | Stability measures for gene rankings |
| GetStabilityDistance-method | Stability measures for gene rankings |
| GetStabilityDistance-methods | Stability measures for gene rankings |
| GetStabilityOverlap | Stability measures for gene lists |
| GetStabilityOverlap-method | Stability measures for gene lists |
| GetStabilityOverlap-methods | Stability measures for gene lists |
| GetStabilityUnion | Stability measures for gene lists |
| GetStabilityUnion-method | Stability measures for gene lists |
| GetStabilityUnion-methods | Stability measures for gene lists |
| HeatmapRankings | Heatmap of genes and rankings |
| HeatmapRankings-method | Heatmap of genes and rankings |
| HeatmapRankings-methods | Heatmap of genes and rankings |
| MergeMethods | Merge rankings obtained from different ranking procedures |
| MergeMethods-method | Merge rankings obtained from different ranking procedures |
| MergeMethods-methods | Merge rankings obtained from different ranking procedures |
| MergeRankings | "RepeatedRanking" |
| MergeRankings-method | "RepeatedRanking" |
| MergeRankings-methods | "RepeatedRanking" |
| overlap | Internal functions |
| plot,RepeatedRanking | "RepeatedRanking" |
| plot-method | "GeneSelectorOutputRanking" |
| plot-method | "RepeatedRanking" |
| plot-method | "StabilityOverlap" |
| plot-method | "StabilityUnion" |
| RankingBaldiLong | Ranking based on the t-statistic of Baldi and Long |
| RankingBaldiLong-method | Ranking based on the t-statistic of Baldi and Long |
| RankingBaldiLong-methods | Ranking based on the t-statistic of Baldi and Long |
| RankingEbam | Ranking based on the empirical Bayes approach of Efron et al. (2001) |
| RankingEbam-method | Ranking based on the empirical Bayes approach of Efron et al. (2001) |
| RankingEbam-methods | Ranking based on the empirical Bayes approach of Efron et al. (2001) |
| RankingFC | Ranking based on the (log) foldchange |
| RankingFC-method | Ranking based on the (log) foldchange |
| RankingFC-methods | Ranking based on the (log) foldchange |
| RankingFoxDimmic | Ranking based on the t-statistic of Fox and Dimmic |
| RankingFoxDimmic-method | Ranking based on the t-statistic of Fox and Dimmic |
| RankingFoxDimmic-methods | Ranking based on the t-statistic of Fox and Dimmic |
| RankingLimma | Ranking based on the 'moderated' t statistic |
| RankingLimma-method | Ranking based on the 'moderated' t statistic |
| RankingLimma-methods | Ranking based on the 'moderated' t statistic |
| RankingPermutation | Ranking based on permutation tests. |
| RankingPermutation-method | Ranking based on permutation tests. |
| RankingPermutation-methods | Ranking based on permutation tests. |
| RankingSam | Ranking based on the SAM statistic |
| RankingSam-method | Ranking based on the SAM statistic |
| RankingSam-methods | Ranking based on the SAM statistic |
| RankingShrinkageT | Ranking based on the 'shrinkage t' statistic |
| RankingShrinkageT-method | Ranking based on the 'shrinkage t' statistic |
| RankingShrinkageT-methods | Ranking based on the 'shrinkage t' statistic |
| RankingSoftthresholdT | Ranking via the 'soft-threshold' t-statistic |
| RankingSoftthresholdT-method | Ranking via the 'soft-threshold' t-statistic |
| RankingSoftthresholdT-methods | Ranking via the 'soft-threshold' t-statistic |
| RankingTstat | Ranking based on the 'ordinary' t statistic. |
| RankingTstat-method | Ranking based on the 'ordinary' t statistic. |
| RankingTstat-methods | Ranking based on the 'ordinary' t statistic. |
| RankingWelchT | Ranking based on the Welch t statistic. |
| RankingWelchT-method | Ranking based on the Welch t statistic. |
| RankingWelchT-methods | Ranking based on the Welch t statistic. |
| RankingWilcEbam | Ranking based on the empirical bayes approach of Efron |
| RankingWilcEbam-method | Ranking based on the empirical bayes approach of Efron |
| RankingWilcEbam-methods | Ranking based on the empirical bayes approach of Efron |
| RankingWilcoxon | Ranking based on the Wilcoxon statistic |
| RankingWilcoxon-method | Ranking based on the Wilcoxon statistic |
| RankingWilcoxon-methods | Ranking based on the Wilcoxon statistic |
| RepeatedRanking | "RepeatedRanking" |
| RepeatedRanking-class | "RepeatedRanking" |
| RepeatRanking | Repeat the ranking procedure for altered data sets |
| RepeatRanking-method | Repeat the ranking procedure for altered data sets |
| RepeatRanking-methods | Repeat the ranking procedure for altered data sets |
| samplingcontrol | Control function |
| SelectedGenes | "GeneSelectorOutputRanking" |
| SelectedGenes-method | "GeneSelectorOutputRanking" |
| SelectedGenes-methods | "GeneSelectorOutputRanking" |
| show-method | "AggregatedRanking" |
| show-method | "BootMatrix" |
| show-method | "FoldMatrix" |
| show-method | "GeneRanking" |
| show-method | "GeneSelectorOutputRanking" |
| show-method | "RepeatedRanking" |
| show-method | "StabilityDistance" |
| show-method | "StabilityOverlap" |
| show-method | "StabilityUnion" |
| StabilityDistance | "StabilityDistance" |
| StabilityDistance-class | "StabilityDistance" |
| StabilityOverlap | "StabilityOverlap" |
| StabilityOverlap-class | "StabilityOverlap" |
| StabilityUnion | "StabilityUnion" |
| StabilityUnion-class | "StabilityUnion" |
| summary-method | "BootMatrix" |
| summary-method | "FoldMatrix" |
| summary-method | "GeneRanking" |
| summary-method | "StabilityDistance" |
| summary-method | "StabilityOverlap" |
| toplist | 'Toplist' methods |
| toplist-method | "AggregatedRanking" |
| toplist-method | "GeneRanking" |
| toplist-method | "GeneSelectorOutputRanking" |
| toplist-method | "RepeatedRanking" |
| toplist-methods | 'Toplist' methods |
| toydata | Simulated gene expression dataset. |
| unioncount | Internal functions |