summary.gsaResult {GiANT}R Documentation

Summarize gene set analysis results

Description

Prints a summary of a gene set analysis result object.

Usage

## S3 method for class 'gsaResult'
summary(object,
		mode = c("summary", "table"),
		orderBy = c("adjustedPValues", "rawPValues", "geneSetName"),
		significantOnly = FALSE,
		signLevel = object$signLevel,
		...)

Arguments

object

A result object as returned by geneSetAnalysis.

mode

Specifies the type of information that is displayed: By default (mode="summary"), a brief summary of the number of significant and insignificant gene sets is printed. For mode="table", createSummaryTable is called, and a detailed table of adjusted and unadjusted p-values and the number of genes for each gene set is printed.

orderBy

If mode="table", this specifies which field should be used for the row ordering. By default, rows are ordered according to the adjusted p-values.

significantOnly

If mode="table", this specifies whether all gene sets (significantOnly=FALSE) or only the statistically significant gene sets (significantOnly=TRUE) should be included in the table.

signLevel

If mode="table" and 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.

...

Currently unused

See Also

geneSetAnalysis, hist.gsaResult, createSummaryTable

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 = 100)

#summarize the analyses
summary(res, mode = "summary")

summary(res, mode = "table", orderBy = "rawPValues")
[Package GiANT version 1.2 Index]