R: Summarize gene set analysis results

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]