AdjustPvalues           P-value adjustment for mutiple testing.
AggregateBayes          Bayesian aggregation of repeated rankings
AggregateBayes-methods
                        Bayesian aggregation of repeated rankings
AggregatePCA            aggregation of repeated rankings by principal
                        components
AggregatePCA-methods    aggregation of repeated rankings by principal
                        components
AggregatePenalty        aggregation of repeated rankings by a variance
                        penalty
AggregatePenalty-methods
                        aggregation of repeated rankings by a variance
                        penalty
AggregateSimple         Simple aggregation of repeated rankings
AggregateSimple-methods
                        'Simple' aggregation of repeated rankings
AggregatedRanking-class
                        "AggregatedRanking"
BootMatrix-class        "BootMatrix"
CombinedRanking-class   "CombinedRanking"
FoldMatrix-class        "FoldMatrix"
GeneRanking-class       "GeneRanking"
GeneSelector            Exclude genes from being candidates for
                        differential expression
GeneSelector-methods    Exclude genes from being candidates for
                        differential expression
GeneSelector-package    Excluding Genes from being candidates for
                        differential expressions by combining various
                        statistics and altered datasets.
GenerateBootMatrix      Altered datasets via bootstrap
GenerateBootMatrix-methods
                        Altered datasets via bootstrap
GenerateFoldMatrix      Altered datasets via k-Jackknife or Label
                        (class) exchange
GenerateFoldMatrix-methods
                        Altered datasets via k-Jackknife or Label
                        (class) exchange
GetAlpha                Helper function for stability assessement.
GetRepeatRanking        Repeat the ranking procedure for altered data
                        sets
GetRepeatRanking-methods
                        Repeat rankings for altered dataset
GetStabilityGLM         Stability measures for significance findings
GetStabilityGLM-methods
                        Stability measures for significance findings
GetStabilityLm          Stability measures for gene rankings
GetStabilityLm-methods
                        Stability measures for gene rankings
GetStabilityOverlap     Stability measures for gene rankings
GetStabilityOverlap-methods
                        Stability measures for gene rankings
GetStabilityPCA         Stability measures for gene rankings
GetStabilityPCA-methods
                        Stability measures for gene rankings
HeatmapMethods          Heatmap of genes and ranking procedures
HeatmapMethods-methods
                        Heatmap of genes and ranking procedures
PCAMethods              Principal Components Analysis for different
                        ranking procedures
PCAMethods-methods      Principal Components Analysis for different
                        ranking procedures
PCAMethodsResult-class
                        "PCAMethodsResult"
RankingBaldiLong        Ranking based on the t-statistic of Baldi and
                        Long
RankingBaldiLong-methods
                        Ranking based on the t-statistic of Baldi and
                        Long
RankingBstat            Ranking based on the B-statistic
RankingBstat-methods    Ranking based on the B-statistic.
RankingEbam             Ranking based on the empirical bayes approach
                        of Efron
RankingEbam-methods     Ranking based on the empirical bayes approach
                        of Efron
RankingFC               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-methods
                        Ranking based on the t-statistic of Fox and
                        Dimmic
RankingGap              Ranking based on 'gaps'
RankingGap-methods      Ranking based on 'gaps'.
RankingLimma            Ranking based on the 'moderated' t statistic
RankingLimma-methods    Ranking based on the 'moderated' t statistic
RankingPermutation      Ranking based on permutation tests.
RankingPermutation-methods
                        Ranking based on permutation tests.
RankingSam              Ranking based on the SAM statistic
RankingSam-methods      Ranking based on the SAM statistic
RankingShrinkageT       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-methods
                        Ranking via the 'soft-threshold' t-statistic
RankingTstat            Ranking based on the 'ordinary' t statistic.
RankingTstat-methods    Ranking with the ordinary t statistic
RankingWelchT           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-methods
                        Ranking based on the empirical bayes approach
                        of Efron
RankingWilcoxon         Ranking based on the Wilcoxon statistic
RankingWilcoxon-methods
                        Ranking based on the Wilcoxon statistic
RecoveryScore           Stability measures for gene rankings
RepeatRanking-class     "RepeatRanking"
StabilityGLM-class      "StabilityGLM"
StabilityLm-class       "StabilityLm"
StabilityOverlap-class
                        "StabilityOverlap"
StabilityPCA-class      "StabilityPCA"
combn                   Internal functions
join                    Combine two objects of class RepeatRankings
join-methods            Combine two objects of class RepeatRankings
plot,AggregatedRanking
                        Visualize results from AggregateBayes
plot,CombinedRanking    Visualize results from GeneSelector
plot,RepeatRanking      Visualize results from GetRepeatRanking
plot,StabilityLm        Visualize results from GetStabilityLm
plot,StabilityOverlap   Visualize results fromGetStabilityOverlap
samplingcontrol         Control function
summary,GeneRanking     Summarize Gene Rankings
summary,StabilityOverlap
                        Summarize Overlap Scores
toplist-methods         'Toplist' methods
toydata                 Simulated gene expression dataset.
variance,RepeatRanking-method
                        Compute genewise variances for ranks
