createSummaryTable: Create an overview table for an analysis

In GiANT: Gene Set Uncertainty in Enrichment Analysis

Description

Creates a data frame summarizing an analysis. This table has one row per gene set, each comprising the adjusted and unadjusted p-values and the number of genes for the set.

Usage

createSummaryTable(object,
		orderBy = c("adjustedPValues", "rawPValues", "geneSetName"),
		significantOnly = FALSE,
		signLevel = object$signLevel)

Arguments

object	A result object as returned by geneSetAnalysis.
orderBy	Specifies which field should be used for the row ordering. By default, rows are ordered according to the adjusted p-values.
significantOnly	Specifies whether all gene sets (significantOnly=FALSE) or only the statistically significant gene sets (significantOnly=TRUE) should be included in the table.
signLevel	If significantOnly=TRUE, this specifies the significance level for the results that should be included in the table. By default, the original significance level of the analysis is used.

Value

A data frame with one row for each included gene set and the columns "adjustedPValues", "rawPValues", "geneSetName" and "geneSetSize". For overrepresentation analyses, there is an additional column "intersectSize" specifying the size of the intersection of the core set and the corresponding gene set.

See Also

geneSetAnalysis, hist.gsaResult, summary

Examples

# load data
require(GlobalAncova)
data(vantVeer)
data(phenodata)
data(pathways)

# perform gene set analyses for several pathways
res <- geneSetAnalysis(
	# global parameters
	dat = vantVeer,
	geneSets = pathways, 
	analysis = analysis.averageCorrelation(), 
	# additional parameters for analysis.averageCorrelation
	labs = phenodata$metastases,
	numSamples = 10)

tab <- createSummaryTable(res)

GiANT documentation built on Oct. 23, 2020, 7:56 p.m.