summary: Summarize gene set analysis results

In GiANT: Gene Set Uncertainty in Enrichment Analysis

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

Value

Returns a data.frame with a summary of the produced results such as data set name, p-values, size of the given gene set.

See Also

geneSetAnalysis, hist.gsaResult, createSummaryTable

Examples

data(exampleData)
  # perform gene set analyses for several pathways
  res <- geneSetAnalysis(
  	# global parameters
  	dat = countdata,
  	geneSets = pathways, 
  	analysis = analysis.averageCorrelation(), 
  	# additional parameters for analysis.averageCorrelation
  	labs = labels,
  	numSamples = 10)
  
  #summarize the analyses
  summary(res, mode = "summary")
  
  summary(res, mode = "table", orderBy = "rawPValues")

GiANT documentation built on Sept. 11, 2024, 9:16 p.m.