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geneSignatureFinder (version 2014.02.17)
A Gene-signatures finder tools
Description
A tool for finding an ensemble gene-signature by a steepest ascending algorithm partially supervised by survival time data.
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Version
2014.02.17
2012.08.20
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Install
install.packages('geneSignatureFinder')
Monthly Downloads
21
Version
2014.02.17
License
GPL-2
Maintainer
Stefano M Pagnotta
Last Published
March 7th, 2014
Functions in geneSignatureFinder (2014.02.17)
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stNSCLC
Survival times of 147 samples affected by Non Small Cell Lung Cancer disease.
goodAndPoorClassification
Function to classify the unsupervised clusters found through a classification procedure in good and poor groups of samples.
signatureFinder
Main function to find the signature.
BHcorrection
Benjamini & Hochberg (1995) method for p-values correction
testGE
Test the differential expression of the the genes in a signature with respect to the good and poor prognosis groups.
BICs
Compute the bayesian information criteria
signatureSummaryTable
Build a data frame populated with the basic information of a signature.
classify
Wrapper function to the classification method
seedsFinder
Evaluate some statistics on all genes in order to select those that can be used as seeds for searching the signatures.
geNSCLC
Gene expression levels on 147 samples affected by Non Small Cell Lung Cancer disease.
NCPUS
Wrapper function to both makeCluster() and detecCore() functions of the 'parallel' library.
removeGeneFrom
Remove the gene with the lowest importance from a signature
importance
Compute an index of importance of the genes in the signature.
searchResultsSummaryTable
Build a data frame populated with the results of a sequential searching of signatures starting from a list of seed-genes.
ensembleTable
Build a data frame populated with statistical indexes for each gene of each signature.
puttingAllTogether
Example of strategy to find signature from different seeds at the same time and to generate plots and summary table.