geneSignatureFinder: A Gene-signatures finder tools

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A tool for finding an ensemble gene-signature by a steepest ascending algorithm partially supervised by survival time data.

Author
Stefano M. Pagnotta, Michele Ceccarelli
Date of publication
2014-03-07 11:58:47
Maintainer
Stefano M. Pagnotta <pagnotta@unisannio.it>
License
GPL-2
Version
2014.02.17
URLs

View on CRAN

Man pages

BHcorrection
Benjamini & Hochberg (1995) method for p-values correction
BICs
Compute the bayesian information criteria
classify
Wrapper function to the classification method
ensembleTable
Build a data frame populated with statistical indexes for...
geNSCLC
Gene expression levels on 147 samples affected by Non Small...
goodAndPoorClassification
Function to classify the unsupervised clusters found through...
importance
Compute an index of importance of the genes in the signature.
NCPUS
Wrapper function to both makeCluster() and detecCore()...
puttingAllTogether
Example of strategy to find signature from different seeds at...
removeGeneFrom
Remove the gene with the lowest importance from a signature
searchResultsSummaryTable
Build a data frame populated with the results of a sequential...
seedsFinder
Evaluate some statistics on all genes in order to select...
signatureFinder
Main function to find the signature.
signatureSummaryTable
Build a data frame populated with the basic information of a...
stNSCLC
Survival times of 147 samples affected by Non Small Cell Lung...
testGE
Test the differential expression of the the genes in a...

Files in this package

geneSignatureFinder
geneSignatureFinder/NAMESPACE
geneSignatureFinder/data
geneSignatureFinder/data/geNSCLC.rda
geneSignatureFinder/data/stNSCLC.rda
geneSignatureFinder/R
geneSignatureFinder/R/print.gSignature.R
geneSignatureFinder/R/goodAndPoorClassification.R
geneSignatureFinder/R/geneSignatureFinder-internal.R
geneSignatureFinder/R/ensembleTable.R
geneSignatureFinder/R/mergeSignatures.R
geneSignatureFinder/R/evaluateGeneSequence.R
geneSignatureFinder/R/puttingAllTogether.R
geneSignatureFinder/R/plot.gSignature.R
geneSignatureFinder/R/signatureFinder.R
geneSignatureFinder/R/pValueFun.R
geneSignatureFinder/R/areDataNotLoaded.R
geneSignatureFinder/R/dMixNorm.R
geneSignatureFinder/R/parallelSignatureFinder.R
geneSignatureFinder/R/searchResultsSummaryTable.R
geneSignatureFinder/R/sequentialSignatureFinder.R
geneSignatureFinder/R/pamUnbiased.R
geneSignatureFinder/R/parallelFindBest.R
geneSignatureFinder/R/testGE.R
geneSignatureFinder/R/removeGeneFrom.R
geneSignatureFinder/R/findBest.R
geneSignatureFinder/R/BICs.R
geneSignatureFinder/R/seedsFinder.R
geneSignatureFinder/R/normalApproximation.R
geneSignatureFinder/R/signatureSummaryTable.R
geneSignatureFinder/R/checkGeneForSeed.R
geneSignatureFinder/R/importance.R
geneSignatureFinder/R/classify.R
geneSignatureFinder/R/BHcorrection.R
geneSignatureFinder/R/NCPUS.R
geneSignatureFinder/R/bbootstrap.R
geneSignatureFinder/R/tValueFun.R
geneSignatureFinder/MD5
geneSignatureFinder/DESCRIPTION
geneSignatureFinder/man
geneSignatureFinder/man/removeGeneFrom.Rd
geneSignatureFinder/man/searchResultsSummaryTable.Rd
geneSignatureFinder/man/BHcorrection.Rd
geneSignatureFinder/man/seedsFinder.Rd
geneSignatureFinder/man/stNSCLC.Rd
geneSignatureFinder/man/classify.Rd
geneSignatureFinder/man/goodAndPoorClassification.Rd
geneSignatureFinder/man/signatureSummaryTable.Rd
geneSignatureFinder/man/signatureFinder.Rd
geneSignatureFinder/man/testGE.Rd
geneSignatureFinder/man/geNSCLC.Rd
geneSignatureFinder/man/ensembleTable.Rd
geneSignatureFinder/man/puttingAllTogether.Rd
geneSignatureFinder/man/NCPUS.Rd
geneSignatureFinder/man/importance.Rd
geneSignatureFinder/man/BICs.Rd