createSummaryTable {GiANT} | R Documentation |
Create an overview table for an 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 |
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 ( |
signLevel |
If |
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
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)
tab <- createSummaryTable(res)