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

In geneSignatureFinder: A Gene-signatures finder tools

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

See Also

signatureFinder, importance, testGE

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)

geneSignatureFinder documentation built on May 2, 2019, 2:32 p.m.