gseaModule {cellHTS2} | R Documentation

## Constructor for an object of class gseaModule

### Description

gseaModule objects encapsulate all the information that is necessary to add the results of a gene set enrichment analysis to a cellHTS report. This feature is still experimental

### Usage

    gseaModule(geneSets, statFuns, scores, annotation)

### Arguments

`geneSets` | An object of class `GeneSetCollection` containing the information about gene sets for which to perform the analysis.
`statFuns` | A list of functions to compute per gene set statistics. These will be called by `applyByCategory` and need to be able to handle two mandatory arguments: `x` are the scores for the respective category, and `y` are all scores of the whole assay. This allows for statistics like `t.test(x,y)`.
`scores` | An optional numeric vector of assay scores. This should be extended to also handle numeric matrices for multi-channel assays.
`annotation` | A `data.frame` with additional annotation for the repsective gene sets.

### Details

The resulting gseaModule object can be supplied as an additional argument to `writeReport`.

This feature is still experimental.

### Value

An object of class gseaModule.

### Author(s)

Florian Hahne

[Package cellHTS2 version 2.44.0 Index]