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GeneSelector (version 2.22.0)

Stability and Aggregation of ranked gene lists

Description

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.

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Version

Version

2.22.0

License

GPL (>= 2)

Maintainer

Martin Slawski

Last Published

February 15th, 2017

Functions in GeneSelector (2.22.0)

AggregateMC

Aggregation of repeated rankings using a Markov chain approach
AggregateSVD

Agregation of repeated rankings using the singular value decomposition (SVD)
FoldMatrix-class

"FoldMatrix"
RankingLimma

Ranking based on the 'moderated' t statistic
RepeatRanking

Repeat the ranking procedure for altered data sets
RankingShrinkageT

Ranking based on the 'shrinkage t' statistic
RankingWilcoxon

Ranking based on the Wilcoxon statistic
GetStabilityDistance

Stability measures for gene rankings
GeneSelectorOutput-class

"GeneSelectorOutputRanking"
StabilityUnion-class

"StabilityUnion"
GenerateFoldMatrix

Altered datasets via k-Jackknife or label exchange
RankingSoftthresholdT

Ranking via the 'soft-threshold' t-statistic
toydata

Simulated gene expression dataset.
RankingEbam

Ranking based on the empirical Bayes approach of Efron et al. (2001)
RankingFC

Ranking based on the (log) foldchange
BootMatrix-class

"BootMatrix"
toplist-methods

'Toplist' methods
internals

Internal functions
MergeMethods

Merge rankings obtained from different ranking procedures
RankingWelchT

Ranking based on the Welch t statistic.
samplingcontrol

Control function
AggregatePenalty

Aggregation of repeated rankings using a variance penalty approach
GenerateBootMatrix

Altered datasets via bootstrap
RankingPermutation

Ranking based on permutation tests.
GeneRanking-class

"GeneRanking"
dispersion,RepeatedRanking

Compute genewise dispersion measures for repeated rankings
GetStabilityUnion

Stability measures for gene lists
RankingWilcEbam

Ranking based on the empirical bayes approach of Efron
StabilityDistance-class

"StabilityDistance"
RankingTstat

Ranking based on the 'ordinary' t statistic.
AggregateSimple

Simple aggregation of repeated rankings
AggregatedRanking-class

"AggregatedRanking"
RankingSam

Ranking based on the SAM statistic
GeneSelector

Select promising candidate genes
GeneSelector-package

Stability and aggregation of ranked gene lists
RepeatedRanking-class

"RepeatedRanking"
StabilityOverlap-class

"StabilityOverlap"
GetStabilityOverlap

Stability measures for gene lists
RankingFoxDimmic

Ranking based on the t-statistic of Fox and Dimmic
HeatmapRankings

Heatmap of genes and rankings
RankingBaldiLong

Ranking based on the t-statistic of Baldi and Long