GeneSelector


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Documentation for package ‘GeneSelector’ version 1.4.0

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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