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.

Author
Martin Slawski <ms@cs.uni-sb.de>, Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>.
Date of publication
None
Maintainer
Martin Slawski <ms@cs.uni-sb.de>
License
GPL (>= 2)
Version
2.24.0

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