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 <firstname.lastname@example.org>, Anne-Laure Boulesteix <email@example.com>.|
|Date of publication||None|
|Maintainer||Martin Slawski <firstname.lastname@example.org>|
|License||GPL (>= 2)|
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...
GenerateBootMatrix: Altered datasets via bootstrap
GenerateFoldMatrix: Altered datasets via k-Jackknife or label exchange
GeneSelector: Select promising candidate genes
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
RepeatRanking: Repeat the ranking procedure for altered data sets
samplingcontrol: Control function
toplist-methods: 'Toplist' methods
toydata: Simulated gene expression dataset.