GeneSelector: Stability and Aggregation of ranked gene lists

The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.

AuthorMartin Slawski <ms@cs.uni-sb.de>, Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>.
Date of publicationNone
MaintainerMartin Slawski <ms@cs.uni-sb.de>
LicenseGPL (>= 2)
Version2.24.0

View on Bioconductor

Man pages

AggregatedRanking-class: "AggregatedRanking"

AggregateMC: Aggregation of repeated rankings using a Markov chain...

AggregatePenalty: Aggregation of repeated rankings using a variance penalty...

AggregateSimple: Simple aggregation of repeated rankings

AggregateSVD: Agregation of repeated rankings using the singular value...

BootMatrix-class: "BootMatrix"

FoldMatrix-class: "FoldMatrix"

GeneRanking-class: "GeneRanking"

GenerateBootMatrix: Altered datasets via bootstrap

GenerateFoldMatrix: Altered datasets via k-Jackknife or label exchange

GeneSelector: Select promising candidate genes

GeneSelectorOutput-class: "GeneSelectorOutputRanking"

GeneSelector-package: Stability and aggregation of ranked gene lists

GetStabilityDistance: Stability measures for gene rankings

GetStabilityOverlap: Stability measures for gene lists

GetStabilityUnion: Stability measures for gene lists

HeatmapRankings: Heatmap of genes and rankings

MergeMethods: Merge rankings obtained from different ranking procedures

RankingBaldiLong: Ranking based on the t-statistic of Baldi and Long

RankingEbam: Ranking based on the empirical Bayes approach of Efron et al....

RankingFC: Ranking based on the (log) foldchange

RankingFoxDimmic: Ranking based on the t-statistic of Fox and Dimmic

RankingLimma: Ranking based on the 'moderated' t statistic

RankingPermutation: Ranking based on permutation tests.

RankingSam: Ranking based on the SAM statistic

RankingShrinkageT: Ranking based on the 'shrinkage t' statistic

RankingSoftthresholdT: Ranking via the 'soft-threshold' t-statistic

RankingTstat: Ranking based on the 'ordinary' t statistic.

RankingWelchT: Ranking based on the Welch t statistic.

RankingWilcEbam: Ranking based on the empirical bayes approach of Efron

RankingWilcoxon: Ranking based on the Wilcoxon statistic

RepeatedRanking-class: "RepeatedRanking"

RepeatRanking: Repeat the ranking procedure for altered data sets

samplingcontrol: Control function

StabilityDistance-class: "StabilityDistance"

StabilityOverlap-class: "StabilityOverlap"

StabilityUnion-class: "StabilityUnion"

toplist-methods: 'Toplist' methods

toydata: Simulated gene expression dataset.

Functions

AggregatedRanking Man page
AggregatedRanking-class Man page
AggregateMC Man page
AggregateMC-methods Man page
AggregateMC,RepeatedRanking-method Man page
AggregatePenalty Man page
AggregatePenalty-methods Man page
AggregatePenalty,RepeatedRanking-method Man page
AggregateSimple Man page
AggregateSimple-methods Man page
AggregateSimple,RepeatedRanking-method Man page
AggregateSVD Man page
AggregateSVD-methods Man page
AggregateSVD,RepeatedRanking-method Man page
BootMatrix Man page
BootMatrix-class Man page
FoldMatrix Man page
FoldMatrix-class Man page
FoldMatrix-method Man page
GeneRanking Man page
GeneRanking-class Man page
GenerateBootMatrix Man page
GenerateBootMatrix,ExpressionSet,character-method Man page
GenerateBootMatrix-methods Man page
GenerateBootMatrix,missing,factor-method Man page
GenerateBootMatrix,missing,numeric-method Man page
GenerateFoldMatrix Man page
GenerateFoldMatrix,ExpressionSet,character-method Man page
GenerateFoldMatrix-methods Man page
GenerateFoldMatrix,missing,factor-method Man page
GenerateFoldMatrix,missing,numeric-method Man page
GeneSelector Man page
GeneSelector,list-method Man page
GeneSelector-methods Man page
GeneSelectorOutput Man page
GeneSelectorOutput-class Man page
GeneSelector-package Man page
GetStabilityDistance Man page
GetStabilityDistance-methods Man page
GetStabilityDistance,RepeatedRanking-method Man page
GetStabilityOverlap Man page
GetStabilityOverlap-methods Man page
GetStabilityOverlap,RepeatedRanking-method Man page
GetStabilityUnion Man page
GetStabilityUnion-methods Man page
GetStabilityUnion,RepeatedRanking-method Man page
HeatmapRankings Man page
HeatmapRankings-methods Man page
HeatmapRankings,RepeatedRanking-method Man page
MergeMethods Man page
MergeMethods,list-method Man page
MergeMethods-methods Man page
MergeRankings Man page
MergeRankings-methods Man page
MergeRankings,RepeatedRanking,RepeatedRanking-method Man page
plot,AggregatedRanking,missing-method Man page
plot,GeneSelectorOutput,missing-method Man page
plot,RepeatedRanking Man page
plot,RepeatedRanking,missing-method Man page
plot,StabilityOverlap,missing-method Man page
plot,StabilityUnion,missing-method Man page
RankingBaldiLong Man page
RankingBaldiLong,ExpressionSet,character-method Man page
RankingBaldiLong,matrix,factor-method Man page
RankingBaldiLong,matrix,numeric-method Man page
RankingBaldiLong-methods Man page
RankingEbam Man page
RankingEbam,ExpressionSet,character-method Man page
RankingEbam,matrix,factor-method Man page
RankingEbam,matrix,numeric-method Man page
RankingEbam-methods Man page
RankingFC Man page
RankingFC,ExpressionSet,character-method Man page
RankingFC,matrix,factor-method Man page
RankingFC,matrix,numeric-method Man page
RankingFC-methods Man page
RankingFoxDimmic Man page
RankingFoxDimmic,ExpressionSet,character-method Man page
RankingFoxDimmic,matrix,factor-method Man page
RankingFoxDimmic,matrix,numeric-method Man page
RankingFoxDimmic-methods Man page
RankingLimma Man page
RankingLimma,ExpressionSet,character-method Man page
RankingLimma,matrix,factor-method Man page
RankingLimma,matrix,numeric-method Man page
RankingLimma-methods Man page
RankingPermutation Man page
RankingPermutation,ExpressionSet,character-method Man page
RankingPermutation,matrix,factor-method Man page
RankingPermutation,matrix,numeric-method Man page
RankingPermutation-methods Man page
RankingSam Man page
RankingSam,ExpressionSet,character-method Man page
RankingSam,matrix,factor-method Man page
RankingSam,matrix,numeric-method Man page
RankingSam-methods Man page
RankingShrinkageT Man page
RankingShrinkageT,ExpressionSet,character-method Man page
RankingShrinkageT,matrix,factor-method Man page
RankingShrinkageT,matrix,numeric-method Man page
RankingShrinkageT-methods Man page
RankingSoftthresholdT Man page
RankingSoftthresholdT,ExpressionSet,character-method Man page
RankingSoftthresholdT,matrix,factor-method Man page
RankingSoftthresholdT,matrix,numeric-method Man page
RankingSoftthresholdT-methods Man page
RankingTstat Man page
RankingTstat,ExpressionSet,character-method Man page
RankingTstat,matrix,factor-method Man page
RankingTstat,matrix,numeric-method Man page
RankingTstat-methods Man page
RankingWelchT Man page
RankingWelchT,ExpressionSet,character-method Man page
RankingWelchT,matrix,factor-method Man page
RankingWelchT,matrix,numeric-method Man page
RankingWelchT-methods Man page
RankingWilcEbam Man page
RankingWilcEbam,ExpressionSet,character-method Man page
RankingWilcEbam,matrix,factor-method Man page
RankingWilcEbam,matrix,numeric-method Man page
RankingWilcEbam-methods Man page
RankingWilcoxon Man page
RankingWilcoxon,ExpressionSet,character-method Man page
RankingWilcoxon,matrix,factor-method Man page
RankingWilcoxon,matrix,numeric-method Man page
RankingWilcoxon-methods Man page
RepeatedRanking Man page
RepeatedRanking-class Man page
RepeatRanking Man page
RepeatRanking,GeneRanking,BootMatrix,missing,missing,missing-met Man page
RepeatRanking,GeneRanking,FoldMatrix,ANY,missing,missing-method Man page
RepeatRanking,GeneRanking,missing,missing,ANY,ANY-method Man page
RepeatRanking-methods Man page
samplingcontrol Man page
SelectedGenes Man page
SelectedGenes,GeneSelectorOutput-method Man page
SelectedGenes-methods Man page
show,AggregatedRanking-method Man page
show,BootMatrix-method Man page
show,FoldMatrix-method Man page
show,GeneRanking-method Man page
show,GeneSelectorOutput-method Man page
show,RepeatedRanking-method Man page
show,StabilityDistance-method Man page
show,StabilityOverlap-method Man page
show,StabilityUnion-method Man page
StabilityDistance Man page
StabilityDistance-class Man page
StabilityOverlap Man page
StabilityOverlap-class Man page
StabilityUnion Man page
StabilityUnion-class Man page
summary,BootMatrix-method Man page
summary,BootMatrix-method Man page
summary,FoldMatrix-method Man page
summary,GeneRanking Man page
summary,GeneRanking-method Man page
summary,StabilityDistance-method Man page
summary,StabilityOverlap-method Man page
toplist Man page
toplist,AggregatedRanking-method Man page
toplist,GeneRanking-method Man page
toplist,GeneSelectorOutput-method Man page
toplist-methods Man page
toplist,RepeatedRanking-method Man page
toydata Man page

Files

GeneSelector/DESCRIPTION
GeneSelector/NAMESPACE
GeneSelector/R
GeneSelector/R/AggregateMC.r
GeneSelector/R/AggregatePenalty.r
GeneSelector/R/AggregateSVD.r
GeneSelector/R/AggregateSimple.r
GeneSelector/R/GeneSelector.r
GeneSelector/R/GenerateBootMatrix.r
GeneSelector/R/GenerateFoldMatrix.r
GeneSelector/R/GetStabilityDistance.r
GeneSelector/R/GetStabilityOverlap.r
GeneSelector/R/GetStabilityUnion.r
GeneSelector/R/HeatmapRankings.r
GeneSelector/R/RankingBaldiLong.r
GeneSelector/R/RankingEbam.r
GeneSelector/R/RankingFC.r
GeneSelector/R/RankingFoxDimmic.r
GeneSelector/R/RankingLimma.r
GeneSelector/R/RankingPermutation.r
GeneSelector/R/RankingSam.r
GeneSelector/R/RankingShrinkageT.r
GeneSelector/R/RankingSoftthresholdT.r
GeneSelector/R/RankingTstat.r
GeneSelector/R/RankingWelchT.r
GeneSelector/R/RankingWilcEbam.r
GeneSelector/R/RankingWilcoxon.r
GeneSelector/R/RepeatRanking.r
GeneSelector/R/classes.r
GeneSelector/R/internals.r
GeneSelector/build
GeneSelector/build/vignette.rds
GeneSelector/data
GeneSelector/data/toydata.rda
GeneSelector/inst
GeneSelector/inst/doc
GeneSelector/inst/doc/GeneSelector.R
GeneSelector/inst/doc/GeneSelector.pdf
GeneSelector/inst/doc/GeneSelector.rnw
GeneSelector/man
GeneSelector/man/AggregateMC.Rd GeneSelector/man/AggregatePenalty.Rd GeneSelector/man/AggregateSVD.Rd GeneSelector/man/AggregateSimple.Rd GeneSelector/man/AggregatedRanking-class.Rd GeneSelector/man/BootMatrix-class.Rd GeneSelector/man/FoldMatrix-class.Rd GeneSelector/man/GeneRanking-class.Rd GeneSelector/man/GeneSelector-package.Rd GeneSelector/man/GeneSelector.Rd GeneSelector/man/GeneSelectorOutput-class.Rd GeneSelector/man/GenerateBootMatrix.Rd GeneSelector/man/GenerateFoldMatrix.Rd GeneSelector/man/GetStabilityDistance.Rd GeneSelector/man/GetStabilityOverlap.Rd GeneSelector/man/GetStabilityUnion.Rd GeneSelector/man/HeatmapRankings.Rd GeneSelector/man/MergeMethods.Rd GeneSelector/man/RankingBaldiLong.Rd GeneSelector/man/RankingEbam.Rd GeneSelector/man/RankingFC.Rd GeneSelector/man/RankingFoxDimmic.Rd GeneSelector/man/RankingLimma.Rd GeneSelector/man/RankingPermutation.Rd GeneSelector/man/RankingSam.Rd GeneSelector/man/RankingShrinkageT.Rd GeneSelector/man/RankingSoftthresholdT.Rd GeneSelector/man/RankingTstat.Rd GeneSelector/man/RankingWelchT.Rd GeneSelector/man/RankingWilcEbam.Rd GeneSelector/man/RankingWilcoxon.Rd GeneSelector/man/RepeatRanking.Rd GeneSelector/man/RepeatedRanking-class.Rd GeneSelector/man/StabilityDistance-class.Rd GeneSelector/man/StabilityOverlap-class.Rd GeneSelector/man/StabilityUnion-class.Rd
GeneSelector/man/dispersion,RepeatedRanking.rd
GeneSelector/man/internals.rd
GeneSelector/man/samplingcontrol.Rd GeneSelector/man/toplist-methods.Rd GeneSelector/man/toydata.Rd
GeneSelector/src
GeneSelector/src/kendall.c
GeneSelector/src/mcfour.c
GeneSelector/src/mct.c
GeneSelector/vignettes
GeneSelector/vignettes/GeneSelector.rnw
GeneSelector/vignettes/literatur.bib
GeneSelector/vignettes/preamble.tex

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