removeGeneFrom: Remove the gene with the lowest importance from a signature
In geneSignatureFinder: A Gene-signatures finder tools

Description Usage Arguments Value Author(s) See Also Examples

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.

1	removeGeneFrom(aSignatureFinder, cutoff = 0)

`aSignatureFinder`	Structure as results from the function signatureFinder()
`cutoff`	is a real value used when the function works iteratively

The function return NULL when no gene is removed, otherwise return a structure as results from the importance() function with the additional slots

`removedGene`	list of genes (as string) removed from the signature
`originalSignature`	same as aSignatureFinder$signature
`originalClassification`	same as aSignatureFinder$classification
`originalTValue`	same as aSignatureFinder$tValue
`originalPValue`	same as aSignatureFinder$pValue

Stefano M. Pagnotta and Michele Ceccarelli

signatureFinder, importance.

data(geNSCLC)
geData <- geNSCLC
data(stNSCLC)
stData <- stNSCLC
# develop the signature
aMakeCluster <- makeCluster(2)
geneSeed <- which(colnames(geData) == "RNF5")
signature <- signatureFinder(geneSeed, cpuCluster = aMakeCluster,
                             stopCpuCluster = FALSE)
signature <- importance(signature, cpuCluster = aMakeCluster)
print(signature$importance)

################################
# 1 step pruning
removeGeneFrom(signature, cutoff = 0.3)$signature

##################################
# iterative pruning of the signature
signature
repeat {
  tmp <- removeGeneFrom(signature, cutoff = 0.3)
  if(is.null(tmp)) break
  signature <- tmp
}  
signature
signature$importance