genesetanalysistable: The server function of the genesetanalysistable module

In pinin4fjords/shinyngs: Shiny apps for NGS data

The server function of the genesetanalysistable module

Description

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

Usage

genesetanalysistable(input, output, session, eselist)

Arguments

input	Input object
output	Output object
session	Session object
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 not called directly, but rather via callModule() (see example). Essentially this just passes the results of colData() applied to the specified SummarizedExperiment object to the simpletable module

Examples

# Example of structures using provided example data

data(zhangneurons)
names(assays(zhangneurons$gene))

# The normalised matrix was used to perform gene set analysis, using 6 types
# of gene set

names(zhangneurons$gene@gene_set_analyses$`normalised-filtered`)

# Gene set can be related back to individual genes via information in the
# containing object's 'gene_sets' slot. These are keyed first to indicate
# which metadata field gene set members pertain to, and secondly by gene
# set type.

names(zhangneurons@gene_sets)

callModule(genesetanalysistable, "genesetanalysistable", eselist)

pinin4fjords/shinyngs documentation built on Feb. 28, 2024, 10:19 a.m.