Stability and Aggregation of ranked gene lists


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Documentation for package ‘GeneSelector’ version 2.2.0

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

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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,RepeatedRanking-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,RepeatedRanking-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,RepeatedRanking-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,RepeatedRanking-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,RepeatedRanking-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,ExpressionSet,character-method Altered datasets via bootstrap
GenerateBootMatrix,missing,factor-method Altered datasets via bootstrap
GenerateBootMatrix,missing,numeric-method Altered datasets via bootstrap
GenerateBootMatrix-methods Altered datasets via bootstrap
GenerateFoldMatrix Altered datasets via k-Jackknife or label exchange
GenerateFoldMatrix,ExpressionSet,character-method Altered datasets via k-Jackknife or label exchange
GenerateFoldMatrix,missing,factor-method Altered datasets via k-Jackknife or label exchange
GenerateFoldMatrix,missing,numeric-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,list-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,RepeatedRanking-method Stability measures for gene rankings
GetStabilityDistance-methods Stability measures for gene rankings
GetStabilityOverlap Stability measures for gene lists
GetStabilityOverlap,RepeatedRanking-method Stability measures for gene lists
GetStabilityOverlap-methods Stability measures for gene lists
GetStabilityUnion Stability measures for gene lists
GetStabilityUnion,RepeatedRanking-method Stability measures for gene lists
GetStabilityUnion-methods Stability measures for gene lists

-- H --

HeatmapRankings Heatmap of genes and rankings
HeatmapRankings,RepeatedRanking-method Heatmap of genes and rankings
HeatmapRankings-methods Heatmap of genes and rankings

-- M --

MergeMethods Merge rankings obtained from different ranking procedures
MergeMethods,list-method Merge rankings obtained from different ranking procedures
MergeMethods-methods Merge rankings obtained from different ranking procedures
MergeRankings "RepeatedRanking"
MergeRankings,RepeatedRanking,RepeatedRanking-method "RepeatedRanking"
MergeRankings-methods "RepeatedRanking"

-- O --

overlap Internal functions

-- P --

plot,GeneSelectorOutput,missing-method "GeneSelectorOutputRanking"
plot,RepeatedRanking "RepeatedRanking"
plot,RepeatedRanking,missing-method "RepeatedRanking"
plot,StabilityOverlap,missing-method "StabilityOverlap"
plot,StabilityUnion,missing-method "StabilityUnion"

-- 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
RankingEbam Ranking based on the empirical Bayes approach of Efron et al. (2001)
RankingEbam,ExpressionSet,character-method Ranking based on the empirical Bayes approach of Efron et al. (2001)
RankingEbam,matrix,factor-method Ranking based on the empirical Bayes approach of Efron et al. (2001)
RankingEbam,matrix,numeric-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,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
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 based on the 'ordinary' t statistic.
RankingTstat,matrix,factor-method Ranking based on the 'ordinary' t statistic.
RankingTstat,matrix,numeric-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,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
RepeatedRanking "RepeatedRanking"
RepeatedRanking-class "RepeatedRanking"
RepeatRanking Repeat the ranking procedure for altered data sets
RepeatRanking,GeneRanking,BootMatrix,missing,missing,missing-method Repeat the ranking procedure for altered data sets
RepeatRanking,GeneRanking,FoldMatrix,ANY,missing,missing-method Repeat the ranking procedure for altered data sets
RepeatRanking,GeneRanking,missing,missing,ANY,ANY-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,GeneSelectorOutput-method "GeneSelectorOutputRanking"
SelectedGenes-methods "GeneSelectorOutputRanking"
show,AggregatedRanking-method "AggregatedRanking"
show,BootMatrix-method "BootMatrix"
show,FoldMatrix-method "FoldMatrix"
show,GeneRanking-method "GeneRanking"
show,GeneSelectorOutput-method "GeneSelectorOutputRanking"
show,RepeatedRanking-method "RepeatedRanking"
show,StabilityDistance-method "StabilityDistance"
show,StabilityOverlap-method "StabilityOverlap"
show,StabilityUnion-method "StabilityUnion"
StabilityDistance "StabilityDistance"
StabilityDistance-class "StabilityDistance"
StabilityOverlap "StabilityOverlap"
StabilityOverlap-class "StabilityOverlap"
StabilityUnion "StabilityUnion"
StabilityUnion-class "StabilityUnion"
summary,BootMatrix-method "BootMatrix"
summary,FoldMatrix-method "FoldMatrix"
summary,GeneRanking-method "GeneRanking"
summary,StabilityDistance-method "StabilityDistance"
summary,StabilityOverlap-method "StabilityOverlap"

-- T --

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

-- U --

unioncount Internal functions