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Last data update: 2014.03.03

R: Build a data frame populated with the results of a sequential...

searchResultsSummaryTable

R Documentation

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

Note

The ratio of the test values in column no.5 measures the improvement of the separation of the survival curves when the classification is based on the signature instead of the starting gene.

Author(s)

Stefano M. Pagnotta and Michele Ceccarelli

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