The server function of the genesetanalysistable module

This module displays gene set analysis tables stored as a list in the gene_set_analyses slot of an ExploratorySummarizedExperiment.

Usage

genesetanalysistable(id, eselist)

Arguments

id

Module namespace

eselist

ExploratorySummarizedExperimentList object containing ExploratorySummarizedExperiment objects

Details

The gene_set_analyses slot must be keyed first by the name of the assay to which it pertains, and second by the gene set type (e.g. 'KEGG'). The containing ExploratorySummarizedExperiment must have a populated gene_sets slot, keyed first by metadata column used to define the gene sets and secondly by the gene set type.

The module is based on the output of roast() from limma, but it's fairly generic, and assumes only the presence of a 'p value' and 'FDR' column, so the output of other methods should be easily adapted to suit.

This function is called directly, using the same id as its UI counterpart, and wraps its logic in moduleServer() (see example). Essentially this just passes the results of colData() applied to the specified SummarizedExperiment object to the simpletable module

Examples

data(airway, package = "airway")
ese <- as(airway, "ExploratorySummarizedExperiment")
eselist <- ExploratorySummarizedExperimentList(ese)
#> Creating ExploratorySummarizedExperimentList object

# This module needs an eselist whose experiments carry gene_set_analyses
# results (see the vignette). Given those, the module server is called like:

if (interactive()) {
  genesetanalysistable("genesetanalysistable", eselist)
}