# Stability and Aggregation of ranked gene lists

## Documentation for package ‘GeneSelector’ version 2.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D F G H M O P R S T U

GeneSelector-package | Stability and aggregation of ranked gene lists

## -- A --

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)

## -- B --

BootMatrix | "BootMatrix"
BootMatrix-class | "BootMatrix"

## -- C --

combn | Internal functions

## -- D --

dispersion | Compute genewise dispersion measures for repeated rankings
dispersion-method | Compute genewise dispersion measures for repeated rankings

## -- F --

FoldMatrix | "FoldMatrix"
FoldMatrix-class | "FoldMatrix"
FoldMatrix-method | "FoldMatrix"

## -- G --

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

## -- H --

HeatmapRankings | Heatmap of genes and rankings
HeatmapRankings-method | Heatmap of genes and rankings
HeatmapRankings-methods | Heatmap of genes and rankings

## -- M --

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"

## -- O --

overlap | Internal functions

## -- P --

plot,RepeatedRanking | "RepeatedRanking"
plot-method | "GeneSelectorOutputRanking"
plot-method | "RepeatedRanking"
plot-method | "StabilityOverlap"
plot-method | "StabilityUnion"

## -- R --

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

## -- S --

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"

## -- T --

toplist | 'Toplist' methods
toplist-method | "AggregatedRanking"
toplist-method | "GeneRanking"
toplist-method | "GeneSelectorOutputRanking"
toplist-method | "RepeatedRanking"
toplist-methods | 'Toplist' methods
toydata | Simulated gene expression dataset.

## -- U --

unioncount | Internal functions