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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

Install

install.packages('geneSignatureFinder')

Monthly Downloads

12

Version

2014.02.17

License

GPL-2

Maintainer

Stefano M Pagnotta

Last Published

March 7th, 2014

Functions in geneSignatureFinder (2014.02.17)

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.