runGSEA-PCOSP-data.frame-method: Run Gene Set Enrichment Analysis On A 'PCOSP' Model Object.

In bhklab/PanCuRx: Pancreatic Ductal Adenocarcinoma Tool-Kit

Description

Run Gene Set Enrichment Analysis On A PCOSP Model Object.

Usage

## S4 method for signature 'PCOSP,data.frame'
runGSEA(object, geneSet, numModels, ..., adjMethod = "fdr", allResults = FALSE)

Arguments

object	A PCOSP model which has been trained with trainModel.
geneSet	A data.frame with two columns, the first being the name of the gene and the second the gene set. The gene names must match the rownames of object. Additional columns will be dropped.
numModels	The number of models to use when selecting the top features from the PCOSP model in object. If missing will default to the top 10% of models.
...	Force subsequent parameters to be named. Not used.
adjMethod	An optional parameter specifying the multiple testing correction to use in piano::runGSAhyper. This parameter must be named.
allResults	Return the full results from piano::runGSAhyper instead of a data.frame of significant results? Default is FALSE. This parameter must be named.

Value

A data.table containing the significantly enriched gene sets.

bhklab/PanCuRx documentation built on Dec. 30, 2021, 4:59 p.m.