gseaModule: Constructor for an object of class gseaModule

In cellHTS2: Analysis of cell-based screens - revised version of cellHTS

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

cellHTS2 documentation built on Nov. 8, 2020, 6 p.m.