summary: Summarize gene set analysis results

In GiANT: Gene Set Uncertainty in Enrichment Analysis

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 = 10)

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

summary(res, mode = "table", orderBy = "rawPValues")

Example output

Loading required package: GlobalAncova
Loading required package: corpcor
Loading required package: globaltest
Loading required package: survival

    Analysis: averageCorrelation

    9 gene set(s) tested:
      - 0 gene set(s) with raw p-value < 0.05
      - min p-value: cell_cycle_control (0.09090909)

    Correction for multiple testing: holm
      - 0 gene set(s) with adjusted p-value < 0.05

                  geneSetName adjustedPValues rawPValues geneSetSize
1          cell_cycle_control       0.8181818 0.09090909          31
2      notch_delta_signalling       1.0000000 0.18181818          34
3              p53_signalling       1.0000000 0.36363636          33
4               wnt_signaling       1.0000000 0.36363636         176
5    tight_junction_signaling       1.0000000 0.54545455         326
6              ras_signalling       1.0000000 0.63636364         266
7                   apoptosis       1.0000000 0.81818182         187
8 androgen_receptor_signaling       1.0000000 0.90909091          72
9          tgf_beta_signaling       1.0000000 0.90909091          82

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