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.

Files in this package

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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