GeneSelector

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