Entry: AdjustPvalues
Aliases: AdjustPvalues
Keywords: univar
Description: P-value adjustment for mutiple testing.
URL: ../../../library/GeneSelector/html/AdjustPvalues.html

Entry: AggregateBayes-methods
Aliases: AggregateBayes-methods AggregateBayes,RepeatRanking,StabilityLm-method AggregateBayes,RepeatRanking,StabilityOverlap-method
Keywords: univar
Description: Bayesian aggregation of repeated rankings
URL: ../../../library/GeneSelector/html/AggregateBayes-methods.html

Entry: AggregateBayes
Aliases: AggregateBayes
Keywords: univar
Description: Bayesian aggregation of repeated rankings
URL: ../../../library/GeneSelector/html/AggregateBayes.html

Entry: AggregatePCA-methods
Aliases: AggregatePCA-methods AggregatePCA,RepeatRanking-method
Keywords: univar
Description: aggregation of repeated rankings by principal components
URL: ../../../library/GeneSelector/html/AggregatePCA-methods.html

Entry: AggregatePCA
Aliases: AggregatePCA
Keywords: univar
Description: aggregation of repeated rankings by principal components
URL: ../../../library/GeneSelector/html/AggregatePCA.html

Entry: AggregatePenalty-methods
Aliases: AggregatePenalty-methods AggregatePenalty,RepeatRanking-method
Keywords: univar
Description: aggregation of repeated rankings by a variance penalty
URL: ../../../library/GeneSelector/html/AggregatePenalty-methods.html

Entry: AggregatePenalty
Aliases: AggregatePenalty
Keywords: univar
Description: aggregation of repeated rankings by a variance penalty
URL: ../../../library/GeneSelector/html/AggregatePenalty.html

Entry: AggregateSimple-methods
Aliases: AggregateSimple-methods AggregateSimple,RepeatRanking,StabilityLm-method AggregateSimple,RepeatRanking,StabilityOverlap-method
Keywords: univar
Description: 'Simple' aggregation of repeated rankings
URL: ../../../library/GeneSelector/html/AggregateSimple-methods.html

Entry: AggregateSimple
Aliases: AggregateSimple
Keywords: univar
Description: Simple aggregation of repeated rankings
URL: ../../../library/GeneSelector/html/AggregateSimple.html

Entry: AggregatedRanking-class
Aliases: AggregatedRanking-class AggregatedRanking show,AggregatedRanking-method
Keywords: univar
Description: "AggregatedRanking"
URL: ../../../library/GeneSelector/html/AggregatedRanking-class.html

Entry: BootMatrix-class
Aliases: BootMatrix-class BootMatrix show,BootMatrix-method summary,BootMatrix-method
Keywords: univar
Description: "BootMatrix"
URL: ../../../library/GeneSelector/html/BootMatrix-class.html

Entry: CombinedRanking-class
Aliases: CombinedRanking-class CombinedRanking show,CombinedRanking-method toplist,CombinedRanking-method SelectedGenes-methods SelectedGenes SelectedGenes,CombinedRanking-method GeneInfoScreen,CombinedRanking-method GeneInfoScreen-methods GeneInfoScreen
Keywords: univar
Description: "CombinedRanking"
URL: ../../../library/GeneSelector/html/CombinedRanking-class.html

Entry: FoldMatrix-class
Aliases: FoldMatrix-class FoldMatrix-method FoldMatrix show,FoldMatrix-method summary,FoldMatrix-method
Keywords: univar
Description: "FoldMatrix"
URL: ../../../library/GeneSelector/html/FoldMatrix-class.html

Entry: GeneRanking-class
Aliases: GeneRanking-class GeneRanking show,GeneRanking-method summary,GeneRanking-method toplist,GeneRanking-method
Keywords: univar
Description: "GeneRanking"
URL: ../../../library/GeneSelector/html/GeneRanking-class.html

Entry: GeneSelector-methods
Aliases: GeneSelector-methods GeneSelector,list-method
Keywords: univar
Description: Exclude genes from being candidates for differential expression
URL: ../../../library/GeneSelector/html/GeneSelector-methods.html

Entry: GeneSelector-package
Aliases: GeneSelector-package
Keywords: univar
Description: Excluding Genes from being candidates for differential expressions by combining various statistics and altered datasets.
URL: ../../../library/GeneSelector/html/GeneSelector-package.html

Entry: GeneSelector
Aliases: GeneSelector
Keywords: univar
Description: Exclude genes from being candidates for differential expression
URL: ../../../library/GeneSelector/html/GeneSelector.html

Entry: GenerateBootMatrix-methods
Aliases: GenerateBootMatrix-methods GenerateBootMatrix,matrix,numeric-method GenerateBootMatrix,matrix,factor-method GenerateBootMatrix,ExpressionSet,character-method
Keywords: univar
Description: Altered datasets via bootstrap
URL: ../../../library/GeneSelector/html/GenerateBootMatrix-methods.html

Entry: GenerateBootMatrix
Aliases: GenerateBootMatrix
Keywords: univar
Description: Altered datasets via bootstrap
URL: ../../../library/GeneSelector/html/GenerateBootMatrix.html

Entry: GenerateFoldMatrix-methods
Aliases: GenerateFoldMatrix-methods GenerateFoldMatrix,matrix,numeric-method GenerateFoldMatrix,matrix,factor-method GenerateFoldMatrix,ExpressionSet,character-method
Keywords: univar
Description: Altered datasets via k-Jackknife or Label (class) exchange
URL: ../../../library/GeneSelector/html/GenerateFoldMatrix-methods.html

Entry: GenerateFoldMatrix
Aliases: GenerateFoldMatrix
Keywords: univar
Description: Altered datasets via k-Jackknife or Label (class) exchange
URL: ../../../library/GeneSelector/html/GenerateFoldMatrix.html

Entry: GetAlpha
Aliases: GetAlpha
Keywords: univar
Description: Helper function for stability assessement.
URL: ../../../library/GeneSelector/html/GetAlpha.html

Entry: GetRepeatRanking-methods
Aliases: GetRepeatRanking-methods GetRepeatRanking,GeneRanking,FoldMatrix,ANY,missing,missing-method GetRepeatRanking,GeneRanking,BootMatrix,missing,missing,missing-method GetRepeatRanking,GeneRanking,missing,missing,ANY,ANY-method
Keywords: univar
Description: Repeat rankings for altered dataset
URL: ../../../library/GeneSelector/html/GetRepeatRanking-methods.html

Entry: GetRepeatRanking
Aliases: GetRepeatRanking
Keywords: univar
Description: Repeat the ranking procedure for altered data sets
URL: ../../../library/GeneSelector/html/GetRepeatRanking.html

Entry: GetStabilityGLM-methods
Aliases: GetStabilityGLM-methods GetStabilityGLM,RepeatRanking-method
Keywords: univar
Description: Stability measures for significance findings
URL: ../../../library/GeneSelector/html/GetStabilityGLM-methods.html

Entry: GetStabilityGLM
Aliases: GetStabilityGLM
Keywords: univar
Description: Stability measures for significance findings
URL: ../../../library/GeneSelector/html/GetStabilityGLM.html

Entry: GetStabilityLm-methods
Aliases: GetStabilityLm-methods GetStabilityLm,RepeatRanking-method
Keywords: univar
Description: Stability measures for gene rankings
URL: ../../../library/GeneSelector/html/GetStabilityLm-methods.html

Entry: GetStabilityLm
Aliases: GetStabilityLm
Keywords: univar
Description: Stability measures for gene rankings
URL: ../../../library/GeneSelector/html/GetStabilityLm.html

Entry: GetStabilityOverlap-methods
Aliases: GetStabilityOverlap-methods GetStabilityOverlap,RepeatRanking-method
Keywords: univar
Description: Stability measures for gene rankings
URL: ../../../library/GeneSelector/html/GetStabilityOverlap-methods.html

Entry: GetStabilityOverlap
Aliases: GetStabilityOverlap
Keywords: univar
Description: Stability measures for gene rankings
URL: ../../../library/GeneSelector/html/GetStabilityOverlap.html

Entry: GetStabilityPCA-methods
Aliases: GetStabilityPCA-methods GetStabilityPCA,RepeatRanking-method
Keywords: univar
Description: Stability measures for gene rankings
URL: ../../../library/GeneSelector/html/GetStabilityPCA-methods.html

Entry: GetStabilityPCA
Aliases: GetStabilityPCA
Keywords: univar
Description: Stability measures for gene rankings
URL: ../../../library/GeneSelector/html/GetStabilityPCA.html

Entry: HeatmapMethods-methods
Aliases: HeatmapMethods-methods HeatmapMethods,list-method
Keywords: univar
Description: Heatmap of genes and ranking procedures
URL: ../../../library/GeneSelector/html/HeatmapMethods-methods.html

Entry: HeatmapMethods
Aliases: HeatmapMethods
Keywords: univar
Description: Heatmap of genes and ranking procedures
URL: ../../../library/GeneSelector/html/HeatmapMethods.html

Entry: PCAMethods-methods
Aliases: PCAMethods-methods PCAMethods,list-method
Keywords: univar
Description: Principal Components Analysis for different ranking procedures
URL: ../../../library/GeneSelector/html/PCAMethods-methods.html

Entry: PCAMethods
Aliases: PCAMethods
Keywords: univar
Description: Principal Components Analysis for different ranking procedures
URL: ../../../library/GeneSelector/html/PCAMethods.html

Entry: PCAMethodsResult-class
Aliases: PCAMethodsResult-class PCAMethodsResult show,PCAMethodsResult-method
Keywords: univar
Description: "PCAMethodsResult"
URL: ../../../library/GeneSelector/html/PCAMethodsResult-class.html

Entry: RankingBaldiLong-methods
Aliases: RankingBaldiLong-methods RankingBaldiLong,matrix,numeric-method RankingBaldiLong,matrix,factor-method RankingBaldiLong,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the t-statistic of Baldi and Long
URL: ../../../library/GeneSelector/html/RankingBaldiLong-methods.html

Entry: RankingBaldiLong
Aliases: RankingBaldiLong
Keywords: univar
Description: Ranking based on the t-statistic of Baldi and Long
URL: ../../../library/GeneSelector/html/RankingBaldiLong.html

Entry: RankingBstat-methods
Aliases: RankingBstat-methods RankingBstat,matrix,numeric-method RankingBstat,matrix,factor-method RankingBstat,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the B-statistic.
URL: ../../../library/GeneSelector/html/RankingBstat-methods.html

Entry: RankingBstat
Aliases: RankingBstat
Keywords: univar
Description: Ranking based on the B-statistic
URL: ../../../library/GeneSelector/html/RankingBstat.html

Entry: RankingEbam-methods
Aliases: RankingEbam-methods RankingEbam,matrix,numeric-method RankingEbam,matrix,factor-method RankingEbam,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the empirical bayes approach of Efron
URL: ../../../library/GeneSelector/html/RankingEbam-methods.html

Entry: RankingEbam
Aliases: RankingEbam
Keywords: univar
Description: Ranking based on the empirical bayes approach of Efron
URL: ../../../library/GeneSelector/html/RankingEbam.html

Entry: RankingFC-methods
Aliases: RankingFC-methods RankingFC,matrix,numeric-method RankingFC,matrix,factor-method RankingFC,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the (log) foldchange
URL: ../../../library/GeneSelector/html/RankingFC-methods.html

Entry: RankingFC
Aliases: RankingFC
Keywords: univar
Description: Ranking based on the (log) foldchange
URL: ../../../library/GeneSelector/html/RankingFC.html

Entry: RankingFoxDimmic-methods
Aliases: RankingFoxDimmic-methods RankingFoxDimmic,matrix,numeric-method RankingFoxDimmic,matrix,factor-method RankingFoxDimmic,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the t-statistic of Fox and Dimmic
URL: ../../../library/GeneSelector/html/RankingFoxDimmic-methods.html

Entry: RankingFoxDimmic
Aliases: RankingFoxDimmic
Keywords: univar
Description: Ranking based on the t-statistic of Fox and Dimmic
URL: ../../../library/GeneSelector/html/RankingFoxDimmic.html

Entry: RankingGap-methods
Aliases: RankingGap-methods RankingGap,matrix,numeric-method RankingGap,matrix,factor-method RankingGap,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on 'gaps'.
URL: ../../../library/GeneSelector/html/RankingGap-methods.html

Entry: RankingGap
Aliases: RankingGap
Keywords: univar
Description: Ranking based on 'gaps'
URL: ../../../library/GeneSelector/html/RankingGap.html

Entry: RankingLimma-methods
Aliases: RankingLimma-methods RankingLimma,matrix,numeric-method RankingLimma,matrix,factor-method RankingLimma,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the 'moderated' t statistic
URL: ../../../library/GeneSelector/html/RankingLimma-methods.html

Entry: RankingLimma
Aliases: RankingLimma
Keywords: univar
Description: Ranking based on the 'moderated' t statistic
URL: ../../../library/GeneSelector/html/RankingLimma.html

Entry: RankingPermutation-methods
Aliases: RankingPermutation-methods RankingPermutation,matrix,numeric-method RankingPermutation,matrix,factor-method RankingPermutation,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on permutation tests.
URL: ../../../library/GeneSelector/html/RankingPermutation-methods.html

Entry: RankingPermutation
Aliases: RankingPermutation
Keywords: univar
Description: Ranking based on permutation tests.
URL: ../../../library/GeneSelector/html/RankingPermutation.html

Entry: RankingSam-methods
Aliases: RankingSam-methods RankingSam,matrix,numeric-method RankingSam,matrix,factor-method RankingSam,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the SAM statistic
URL: ../../../library/GeneSelector/html/RankingSam-methods.html

Entry: RankingSam
Aliases: RankingSam
Keywords: univar
Description: Ranking based on the SAM statistic
URL: ../../../library/GeneSelector/html/RankingSam.html

Entry: RankingShrinkageT-methods
Aliases: RankingShrinkageT-methods RankingShrinkageT,matrix,numeric-method RankingShrinkageT,matrix,factor-method RankingShrinkageT,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the 'shrinkage t' statistic
URL: ../../../library/GeneSelector/html/RankingShrinkageT-methods.html

Entry: RankingShrinkageT
Aliases: RankingShrinkageT
Keywords: univar
Description: Ranking based on the 'shrinkage t' statistic
URL: ../../../library/GeneSelector/html/RankingShrinkageT.html

Entry: RankingSoftthresholdT-methods
Aliases: RankingSoftthresholdT-methods RankingSoftthresholdT,matrix,numeric-method RankingSoftthresholdT,matrix,factor-method RankingSoftthresholdT,ExpressionSet,character-method
Keywords: univar
Description: Ranking via the 'soft-threshold' t-statistic
URL: ../../../library/GeneSelector/html/RankingSoftthresholdT-methods.html

Entry: RankingSoftthresholdT
Aliases: RankingSoftthresholdT
Keywords: univar
Description: Ranking via the 'soft-threshold' t-statistic
URL: ../../../library/GeneSelector/html/RankingSoftthresholdT.html

Entry: RankingTstat-methods
Aliases: RankingTstat-methods RankingTstat,matrix,numeric-method RankingTstat,matrix,factor-method RankingTstat,ExpressionSet,character-method
Keywords: univar
Description: Ranking with the ordinary t statistic
URL: ../../../library/GeneSelector/html/RankingTstat-methods.html

Entry: RankingTstat
Aliases: RankingTstat
Keywords: univar
Description: Ranking based on the 'ordinary' t statistic.
URL: ../../../library/GeneSelector/html/RankingTstat.html

Entry: RankingWelchT-methods
Aliases: RankingWelchT-methods RankingWelchT,matrix,numeric-method RankingWelchT,matrix,factor-method RankingWelchT,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the Welch t statistic.
URL: ../../../library/GeneSelector/html/RankingWelchT-methods.html

Entry: RankingWelchT
Aliases: RankingWelchT
Keywords: univar
Description: Ranking based on the Welch t statistic.
URL: ../../../library/GeneSelector/html/RankingWelchT.html

Entry: RankingWilcEbam-methods
Aliases: RankingWilcEbam-methods RankingWilcEbam,matrix,numeric-method RankingWilcEbam,matrix,factor-method RankingWilcEbam,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the empirical bayes approach of Efron
URL: ../../../library/GeneSelector/html/RankingWilcEbam-methods.html

Entry: RankingWilcEbam
Aliases: RankingWilcEbam
Keywords: univar
Description: Ranking based on the empirical bayes approach of Efron
URL: ../../../library/GeneSelector/html/RankingWilcEbam.html

Entry: RankingWilcoxon-methods
Aliases: RankingWilcoxon-methods RankingWilcoxon,matrix,numeric-method RankingWilcoxon,matrix,factor-method RankingWilcoxon,ExpressionSet,character-method
Keywords: univar
Description: Ranking based on the Wilcoxon statistic
URL: ../../../library/GeneSelector/html/RankingWilcoxon-methods.html

Entry: RankingWilcoxon
Aliases: RankingWilcoxon
Keywords: univar
Description: Ranking based on the Wilcoxon statistic
URL: ../../../library/GeneSelector/html/RankingWilcoxon.html

Entry: RecoveryScore
Aliases: RecoveryScore
Keywords: univar
Description: Stability measures for gene rankings
URL: ../../../library/GeneSelector/html/RecoveryScore.html

Entry: RepeatRanking-class
Aliases: RepeatRanking-class RepeatRanking show,RepeatRanking-method toplist,RepeatRanking-method
Keywords: univar
Description: "RepeatRanking"
URL: ../../../library/GeneSelector/html/RepeatRanking-class.html

Entry: StabilityGLM-class
Aliases: StabilityGLM-class StabilityGLM show,StabilityGLM-method
Keywords: univar
Description: "StabilityGLM"
URL: ../../../library/GeneSelector/html/StabilityGLM-class.html

Entry: StabilityLm-class
Aliases: StabilityLm-class StabilityLm show,StabilityLm-method
Keywords: univar
Description: "StabilityLm"
URL: ../../../library/GeneSelector/html/StabilityLm-class.html

Entry: StabilityOverlap-class
Aliases: StabilityOverlap-class StabilityOverlap show,StabilityOverlap-method summary,StabilityOverlap-method
Keywords: univar
Description: "StabilityOverlap"
URL: ../../../library/GeneSelector/html/StabilityOverlap-class.html

Entry: StabilityPCA-class
Aliases: StabilityPCA-class StabilityPCA show,StabilityPCA-method
Keywords: univar
Description: "StabilityPCA"
URL: ../../../library/GeneSelector/html/StabilityPCA-class.html

Entry: internals
Aliases: combn overlap posterior1 posterior2 posterior3 posterior4 getLambda characterplot
Keywords: univar
Description: Internal functions
URL: ../../../library/GeneSelector/html/internals.html

Entry: join-methods
Aliases: join-methods join,RepeatRanking,RepeatRanking-method
Keywords: univar
Description: Combine two objects of class RepeatRankings
URL: ../../../library/GeneSelector/html/join-methods.html

Entry: join
Aliases: join
Keywords: univar
Description: Combine two objects of class RepeatRankings
URL: ../../../library/GeneSelector/html/join.html

Entry: plot,AggregatedRanking
Aliases: plot,AggregatedRanking plot,AggregatedRanking,missing-method
Keywords: univar
Description: Visualize results from AggregateBayes
URL: ../../../library/GeneSelector/html/plot,AggregatedRanking.html

Entry: plot,CombinedRanking
Aliases: plot,CombinedRanking plot,CombinedRanking,missing-method
Keywords: univar
Description: Visualize results from GeneSelector
URL: ../../../library/GeneSelector/html/plot,CombinedRanking.html

Entry: plot,RepeatRanking
Aliases: plot,RepeatRanking plot,RepeatRanking,missing-method
Keywords: univar
Description: Visualize results from GetRepeatRanking
URL: ../../../library/GeneSelector/html/plot,RepeatRanking.html

Entry: plot,StabilityLm
Aliases: plot,StabilityLm plot,StabilityLm,missing-method
Keywords: univar
Description: Visualize results from GetStabilityLm
URL: ../../../library/GeneSelector/html/plot,StabilityLm.html

Entry: plot,StabilityOverlap
Aliases: plot,StabilityOverlap plot,StabilityOverlap,missing-method
Keywords: univar
Description: Visualize results fromGetStabilityOverlap
URL: ../../../library/GeneSelector/html/plot,StabilityOverlap.html

Entry: samplingcontrol
Aliases: samplingcontrol
Keywords: univar
Description: Control function
URL: ../../../library/GeneSelector/html/samplingcontrol.html

Entry: summary,GeneRanking
Aliases: summary,GeneRanking
Keywords: univar
Description: Summarize Gene Rankings
URL: ../../../library/GeneSelector/html/summary,GeneRanking.html

Entry: summary,StabilityOverlap
Aliases: summary,StabilityOverlap
Keywords: univar
Description: Summarize Overlap Scores
URL: ../../../library/GeneSelector/html/summary,StabilityOverlap.html

Entry: toplist-methods
Aliases: toplist-methods toplist
Keywords: univar
Description: 'Toplist' methods
URL: ../../../library/GeneSelector/html/toplist-methods.html

Entry: toydata
Aliases: toydata
Keywords: univar
Description: Simulated gene expression dataset.
URL: ../../../library/GeneSelector/html/toydata.html

Entry: variance,RepeatRanking
Aliases: variance,RepeatRanking-method variance
Keywords: univar
Description: Compute genewise variances for ranks
URL: ../../../library/GeneSelector/html/variance,RepeatRanking.html
