Stability and Aggregation of ranked gene lists

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

-- --

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