Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/searchResultsSummaryTable.R

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

1 | ```
searchResultsSummaryTable(aSearchResults)
``` |

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

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 |

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.

Stefano M. Pagnotta and Michele Ceccarelli

`help`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
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
``` |

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