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 |