GeneSelector-package {GeneSelector} | R Documentation |
Excluding Genes from being candidates for differential
expressions by combining various statistics and altered datasets.
Description
The name 'Geneselector' stands for the exclusion
of genes that might be considered differentially
expressed. 'Selected' genes are those present
at the top of the list in various featured ranking
methods (currently 15). In addition, the stability
of the findings are checked by creating perturbed
versions of the original dataset, e.g. by leaving
samples, swapping class labels, generating bootstrap
replicates or adding noise.
Details
Package: | GeneSelector |
Type: | Package |
Version: | 0.9.5 |
Date: | 2008-31-1 |
License: | GPL (version 2 or later) |
Most Important Steps for the workflow are:
- 1.
- Generate a Gene Ranking with RankingTstat,
RankingFC, RankingWelchT, RankingWilcoxon,
RankingBaldiLong, RankingFoxDimmic,
RankingLimma, RankingEbam, RankingWilcEbam,
RankingSam, RankingBstat, RankingShrinkageT,
RankingSoftthresholdT, RankingPermutation,
RankingGap
- 2.
- Inspect the toplist using
toplist
.
- 3.
- Prepare altered datasets using GenerateFoldMatrix or
GenerateBootMatrix
- 4.
- Get rankings for the altered datasets with GetRepeatRanking.
- 5.
- Assess stability of rankings using GetStabilityLm,
GetStabilityOverlap, RecoveryScore.
- 6.
- Aggregate different rankings with a bayesian approach
with AggregateBayes or in a simple manner
(AggregateSimple).
- 7.
- Inspect visually the similarity of methods using HeatmapMethods.
- 8.
- Combine everything into the GeneSelector.
Author(s)
Martin Slawski martin.slawski@campus.lmu.de,
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix
Maintainer: Martin Slawski martin.slawski@campus.lmu.de.
[Package
GeneSelector version 1.2.0
Index]