R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Build a data frame populated with the basic information of a...

signatureSummaryTable

R Documentation

Build a data frame populated with the basic information of a signature.

Description

A table with as many rows as the number of genes belonging to the signature.

Usage

signatureSummaryTable(aSignatureFinder)

Arguments

aSignatureFinder

Structure as results from the signatureFinder() function

Value

A data frame with the following columns

`column no.1`	genes in the signature
`column no.2`	percentage of missing data per gene
`column no.3`	importance (if computed)
`column no.4`	median level in good prognosis group (if computed)
`column no.5`	median level in poor prognosis group (if computed)
`column no.6`	mean level in good prognosis group (if computed)
`column no.7`	mean level in poor prognosis group (if computed)
`column no.8`	absolute difference of the mean levels (if computed)
`column no.9`	Welch's test-Value (if computed)
`column no.10`	p-value associated to t-value (if computed; see testGE() function)

Author(s)

Stefano M. Pagnotta and Michele Ceccarelli

Examples

data(geNSCLC)
geData <- geNSCLC
data(stNSCLC)
stData <- stNSCLC
# set the dimension of the cpu's cluster (use a value different from 2 
# depending on the number of cpu avalilable)
aMakeCluster <- makeCluster(2)
signature <- signatureFinder(which(colnames(geData) == "HIF1a"),
  cpuCluster = aMakeCluster)
signature <- importance(signature)
signature <- testGE(signature)
signatureTable <- signatureSummaryTable(signature)
print(signatureTable)