geneSignatureFinder (version 2014.02.17)

searchResultsSummaryTable: Build a data frame populated with the results of a sequential searching of signatures starting from a list of seed-genes.

Description

The data frame contains as many rows as the list of seed-genes and six columns as described in the value section.

Usage

searchResultsSummaryTable(aSearchResults)

Arguments

aSearchResults

is a list of the signatures computed from a list of seed-genes. See the example.

Value

• A data frame with the following columns
• column no.1
  starting/seed-gene.
• column no.2
  number of genes in the signature.
• column no.3
  test value of the log-rank test for the survival curves associated to the good and poor prognosis groups.
• column no.4
  log(p-value)/log(10), the p-value is the one corresponding to the test value of the log-rank test.
• column no.5
  ratio of the test values of the log-rank test computed with respect to the clustering given by the starting gene and the clustering generated by the signature
• column no.6
  genes in the signature

See Also

help.

Examples

data(geNSCLC)
geData <- geNSCLC
data(stNSCLC)
stData <- stNSCLC

# CALCA = 152, SELP = 115
seedGenes <- c(152, 115)
K <- length(seedGenes)
searchResults <- vector("list", K)
names(searchResults) <- colnames(geData)[seedGenes]


aMakeCluster <- makeCluster(2)
for(k in 1:K) 
  searchResults[[k]] <- signatureFinder(seedGenes[k], 
    cpuCluster = aMakeCluster, stopCpuCluster = FALSE)
stopCluster(aMakeCluster)
searchResults
signaturesTable <- searchResultsSummaryTable(searchResults)
signaturesTable