A Gene-signatures finder tools

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Documentation for package ‘geneSignatureFinder’ version 2014.02.17

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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 each gene of each signature.
geNSCLC Gene expression levels on 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.
importance Compute an index of importance of the genes in the signature.
NCPUS Wrapper function to both makeCluster() and detecCore() functions of the 'parallel' library.
puttingAllTogether Example of strategy to find signature from different seeds at the same time and to generate plots and summary table.
removeGeneFrom Remove the gene with the lowest importance from a signature
searchResultsSummaryTable Build a data frame populated with the results of a sequential searching of signatures starting from a list of seed-genes.
seedsFinder Evaluate some statistics on all genes in order to select those that can be used as seeds for searching the signatures.
signatureFinder Main function to find the signature.
signatureSummaryTable Build a data frame populated with the basic information of a signature.
stNSCLC Survival times of 147 samples affected by Non Small Cell Lung Cancer disease.
testGE Test the differential expression of the the genes in a signature with respect to the good and poor prognosis groups.