removeGeneFrom
(Package: geneSignatureFinder) :
Remove the gene with the lowest importance from a signature
This function implements a pruning algorithm devoted to remove the gene with the lowest importance from the signature. The importances have to be computed before calling this function. The gene with the lowest importance is removed and the set of importances are computed again. The function is designed to be used iteratively so that all the genes with importance below a cutoff value are removed. If the signature has the results of the testGEL() function just computed, they are removed.
● Data Source:
CranContrib
● Keywords:
● Alias: removeGeneFrom
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The data frame contains as many rows as the list of seed-genes and six columns as described in the value section.
● Data Source:
CranContrib
● Keywords:
● Alias: searchResultsSummaryTable
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BHcorrection
(Package: geneSignatureFinder) :
Benjamini & Hochberg (1995) method for p-values correction
This function evaluate the p-values correction according to the Benjamini & Hochberg (1995) method.
● Data Source:
CranContrib
● Keywords:
● Alias: BHcorrection
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seedsFinder
(Package: geneSignatureFinder) :
Evaluate some statistics on all genes in order to select those that can
This function works on each column (gene expression level) of the geData and returns the test-value and p-value of the log-rank test, the bayesian information criterion value under the hypothesis that tha data are drawn from a single gaussian (bic1) and a mixture of two gaussians (bic2); at the end the clustering of the samples is added.
● Data Source:
CranContrib
● Keywords:
● Alias: seedsFinder
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classify
(Package: geneSignatureFinder) :
Wrapper function to the classification method
This function links the classification method to the procedures to find the seed genes and the signatures. If necessary this function can be rewritten in order to use a different classification method. Actually the classification method linked is the partitioning around medoids (see pam() function for details)
● Data Source:
CranContrib
● Keywords:
● Alias: classify
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This function label the groups found by the unsupervised classification in good and poor.
● Data Source:
CranContrib
● Keywords:
● Alias: goodAndPoorClassification
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signatureSummaryTable
(Package: geneSignatureFinder) :
Build a data frame populated with the basic information of a signature.
A table with as many rows as the number of genes belonging to the signature.
● Data Source:
CranContrib
● Keywords:
● Alias: signatureSummaryTable
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This function implements the algorithm to find the signature using a searching strategy supervised by survival time data.
● Data Source:
CranContrib
● Keywords:
● Alias: signatureFinder
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testGE
(Package: geneSignatureFinder) :
Test the differential expression of the the genes in a signature with respect to the good and poor prognosis groups.
Given the clustering of the samples in good and poor prognosis associated to the signature, for each gene in the signature the test for the null hypothesis of equality of the expression levels is performed. Additional statistics are provided.
● Data Source:
CranContrib
● Keywords:
● Alias: testGE
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ensembleTable
(Package: geneSignatureFinder) :
Build a data frame populated with statistical indexes for each gene of each signature.
Its a summary table from which the ensemble signature is obtained.
● Data Source:
CranContrib
● Keywords:
● Alias: ensembleTable
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providing 
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