# GeneSelector

## Documentation for package ‘GeneSelector’ version 1.2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C F G H J O P R S T V

## -- --

GeneSelector-package | Excluding Genes from being candidates for differential expressions by combining various statistics and altered datasets.

## -- A --

AdjustPvalues | P-value adjustment for mutiple testing.
AggregateBayes | Bayesian aggregation of repeated rankings
AggregateBayes,RepeatRanking,StabilityLm-method | Bayesian aggregation of repeated rankings
AggregateBayes,RepeatRanking,StabilityOverlap-method | Bayesian aggregation of repeated rankings
AggregateBayes-methods | Bayesian aggregation of repeated rankings
AggregatedRanking | "AggregatedRanking"
AggregatedRanking-class | "AggregatedRanking"
AggregatePCA | aggregation of repeated rankings by principal components
AggregatePCA,RepeatRanking-method | 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,RepeatRanking-method | 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,RepeatRanking,StabilityLm-method | 'Simple' aggregation of repeated rankings
AggregateSimple,RepeatRanking,StabilityOverlap-method | 'Simple' aggregation of repeated rankings
AggregateSimple-methods | 'Simple' aggregation of repeated rankings

## -- B --

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

## -- C --

characterplot | Internal functions
CombinedRanking | "CombinedRanking"
CombinedRanking-class | "CombinedRanking"
combn | Internal functions

## -- F --

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

## -- G --

GeneInfoScreen | "CombinedRanking"
GeneInfoScreen,CombinedRanking-method | "CombinedRanking"
GeneInfoScreen-methods | "CombinedRanking"
GeneRanking | "GeneRanking"
GeneRanking-class | "GeneRanking"
GenerateBootMatrix | Altered datasets via bootstrap
GenerateBootMatrix,ExpressionSet,character-method | Altered datasets via bootstrap
GenerateBootMatrix,matrix,factor-method | Altered datasets via bootstrap
GenerateBootMatrix,matrix,numeric-method | Altered datasets via bootstrap
GenerateBootMatrix-methods | Altered datasets via bootstrap
GenerateFoldMatrix | Altered datasets via k-Jackknife or Label (class) exchange
GenerateFoldMatrix,ExpressionSet,character-method | Altered datasets via k-Jackknife or Label (class) exchange
GenerateFoldMatrix,matrix,factor-method | Altered datasets via k-Jackknife or Label (class) exchange
GenerateFoldMatrix,matrix,numeric-method | Altered datasets via k-Jackknife or Label (class) exchange
GenerateFoldMatrix-methods | Altered datasets via k-Jackknife or Label (class) exchange
GeneSelector | Exclude genes from being candidates for differential expression
GeneSelector,list-method | Exclude genes from being candidates for differential expression
GeneSelector-methods | Exclude genes from being candidates for differential expression
GetAlpha | Helper function for stability assessement.
getLambda | Internal functions
GetRepeatRanking | Repeat the ranking procedure for altered data sets
GetRepeatRanking,GeneRanking,BootMatrix,missing,missing,missing-method | Repeat rankings for altered dataset
GetRepeatRanking,GeneRanking,FoldMatrix,ANY,missing,missing-method | Repeat rankings for altered dataset
GetRepeatRanking,GeneRanking,missing,missing,ANY,ANY-method | Repeat rankings for altered dataset
GetRepeatRanking-methods | Repeat rankings for altered dataset
GetStabilityGLM | Stability measures for significance findings
GetStabilityGLM,RepeatRanking-method | Stability measures for significance findings
GetStabilityGLM-methods | Stability measures for significance findings
GetStabilityLm | Stability measures for gene rankings
GetStabilityLm,RepeatRanking-method | Stability measures for gene rankings
GetStabilityLm-methods | Stability measures for gene rankings
GetStabilityOverlap | Stability measures for gene rankings
GetStabilityOverlap,RepeatRanking-method | Stability measures for gene rankings
GetStabilityOverlap-methods | Stability measures for gene rankings
GetStabilityPCA | Stability measures for gene rankings
GetStabilityPCA,RepeatRanking-method | Stability measures for gene rankings
GetStabilityPCA-methods | Stability measures for gene rankings

## -- H --

HeatmapMethods | Heatmap of genes and ranking procedures
HeatmapMethods,list-method | Heatmap of genes and ranking procedures
HeatmapMethods-methods | Heatmap of genes and ranking procedures

## -- J --

join | Combine two objects of class RepeatRankings
join,RepeatRanking,RepeatRanking-method | Combine two objects of class RepeatRankings
join-methods | Combine two objects of class RepeatRankings

## -- O --

overlap | Internal functions

## -- P --

PCAMethods | Principal Components Analysis for different ranking procedures
PCAMethods,list-method | Principal Components Analysis for different ranking procedures
PCAMethods-methods | Principal Components Analysis for different ranking procedures
PCAMethodsResult | "PCAMethodsResult"
PCAMethodsResult-class | "PCAMethodsResult"
plot,AggregatedRanking | Visualize results from AggregateBayes
plot,AggregatedRanking,missing-method | Visualize results from AggregateBayes
plot,CombinedRanking | Visualize results from GeneSelector
plot,CombinedRanking,missing-method | Visualize results from GeneSelector
plot,RepeatRanking | Visualize results from GetRepeatRanking
plot,RepeatRanking,missing-method | Visualize results from GetRepeatRanking
plot,StabilityLm | Visualize results from GetStabilityLm
plot,StabilityLm,missing-method | Visualize results from GetStabilityLm
plot,StabilityOverlap | Visualize results fromGetStabilityOverlap
plot,StabilityOverlap,missing-method | Visualize results fromGetStabilityOverlap
posterior1 | Internal functions
posterior2 | Internal functions
posterior3 | Internal functions
posterior4 | Internal functions

## -- R --

RankingBaldiLong | Ranking based on the t-statistic of Baldi and Long
RankingBaldiLong,ExpressionSet,character-method | Ranking based on the t-statistic of Baldi and Long
RankingBaldiLong,matrix,factor-method | Ranking based on the t-statistic of Baldi and Long
RankingBaldiLong,matrix,numeric-method | 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,ExpressionSet,character-method | Ranking based on the B-statistic.
RankingBstat,matrix,factor-method | Ranking based on the B-statistic.
RankingBstat,matrix,numeric-method | 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,ExpressionSet,character-method | Ranking based on the empirical bayes approach of Efron
RankingEbam,matrix,factor-method | Ranking based on the empirical bayes approach of Efron
RankingEbam,matrix,numeric-method | 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,ExpressionSet,character-method | Ranking based on the (log) foldchange
RankingFC,matrix,factor-method | Ranking based on the (log) foldchange
RankingFC,matrix,numeric-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,ExpressionSet,character-method | Ranking based on the t-statistic of Fox and Dimmic
RankingFoxDimmic,matrix,factor-method | Ranking based on the t-statistic of Fox and Dimmic
RankingFoxDimmic,matrix,numeric-method | 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,ExpressionSet,character-method | Ranking based on 'gaps'.
RankingGap,matrix,factor-method | Ranking based on 'gaps'.
RankingGap,matrix,numeric-method | Ranking based on 'gaps'.
RankingGap-methods | Ranking based on 'gaps'.
RankingLimma | Ranking based on the 'moderated' t statistic
RankingLimma,ExpressionSet,character-method | Ranking based on the 'moderated' t statistic
RankingLimma,matrix,factor-method | Ranking based on the 'moderated' t statistic
RankingLimma,matrix,numeric-method | Ranking based on the 'moderated' t statistic
RankingLimma-methods | Ranking based on the 'moderated' t statistic
RankingPermutation | Ranking based on permutation tests.
RankingPermutation,ExpressionSet,character-method | Ranking based on permutation tests.
RankingPermutation,matrix,factor-method | Ranking based on permutation tests.
RankingPermutation,matrix,numeric-method | Ranking based on permutation tests.
RankingPermutation-methods | Ranking based on permutation tests.
RankingSam | Ranking based on the SAM statistic
RankingSam,ExpressionSet,character-method | Ranking based on the SAM statistic
RankingSam,matrix,factor-method | Ranking based on the SAM statistic
RankingSam,matrix,numeric-method | Ranking based on the SAM statistic
RankingSam-methods | Ranking based on the SAM statistic
RankingShrinkageT | Ranking based on the 'shrinkage t' statistic
RankingShrinkageT,ExpressionSet,character-method | Ranking based on the 'shrinkage t' statistic
RankingShrinkageT,matrix,factor-method | Ranking based on the 'shrinkage t' statistic
RankingShrinkageT,matrix,numeric-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,ExpressionSet,character-method | Ranking via the 'soft-threshold' t-statistic
RankingSoftthresholdT,matrix,factor-method | Ranking via the 'soft-threshold' t-statistic
RankingSoftthresholdT,matrix,numeric-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,ExpressionSet,character-method | Ranking with the ordinary t statistic
RankingTstat,matrix,factor-method | Ranking with the ordinary t statistic
RankingTstat,matrix,numeric-method | Ranking with the ordinary t statistic
RankingTstat-methods | Ranking with the ordinary t statistic
RankingWelchT | Ranking based on the Welch t statistic.
RankingWelchT,ExpressionSet,character-method | Ranking based on the Welch t statistic.
RankingWelchT,matrix,factor-method | Ranking based on the Welch t statistic.
RankingWelchT,matrix,numeric-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,ExpressionSet,character-method | Ranking based on the empirical bayes approach of Efron
RankingWilcEbam,matrix,factor-method | Ranking based on the empirical bayes approach of Efron
RankingWilcEbam,matrix,numeric-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,ExpressionSet,character-method | Ranking based on the Wilcoxon statistic
RankingWilcoxon,matrix,factor-method | Ranking based on the Wilcoxon statistic
RankingWilcoxon,matrix,numeric-method | Ranking based on the Wilcoxon statistic
RankingWilcoxon-methods | Ranking based on the Wilcoxon statistic
RecoveryScore | Stability measures for gene rankings
RepeatRanking | "RepeatRanking"
RepeatRanking-class | "RepeatRanking"

## -- S --

samplingcontrol | Control function
SelectedGenes | "CombinedRanking"
SelectedGenes,CombinedRanking-method | "CombinedRanking"
SelectedGenes-methods | "CombinedRanking"
show,AggregatedRanking-method | "AggregatedRanking"
show,BootMatrix-method | "BootMatrix"
show,CombinedRanking-method | "CombinedRanking"
show,FoldMatrix-method | "FoldMatrix"
show,GeneRanking-method | "GeneRanking"
show,PCAMethodsResult-method | "PCAMethodsResult"
show,RepeatRanking-method | "RepeatRanking"
show,StabilityGLM-method | "StabilityGLM"
show,StabilityLm-method | "StabilityLm"
show,StabilityOverlap-method | "StabilityOverlap"
show,StabilityPCA-method | "StabilityPCA"
StabilityGLM | "StabilityGLM"
StabilityGLM-class | "StabilityGLM"
StabilityLm | "StabilityLm"
StabilityLm-class | "StabilityLm"
StabilityOverlap | "StabilityOverlap"
StabilityOverlap-class | "StabilityOverlap"
StabilityPCA | "StabilityPCA"
StabilityPCA-class | "StabilityPCA"
summary,BootMatrix-method | "BootMatrix"
summary,FoldMatrix-method | "FoldMatrix"
summary,GeneRanking | Summarize Gene Rankings
summary,GeneRanking-method | "GeneRanking"
summary,StabilityOverlap | Summarize Overlap Scores
summary,StabilityOverlap-method | "StabilityOverlap"

## -- T --

toplist | 'Toplist' methods
toplist,CombinedRanking-method | "CombinedRanking"
toplist,GeneRanking-method | "GeneRanking"
toplist,RepeatRanking-method | "RepeatRanking"
toplist-methods | 'Toplist' methods
toydata | Simulated gene expression dataset.

## -- V --

variance | Compute genewise variances for ranks
variance,RepeatRanking-method | Compute genewise variances for ranks