mod_gsea: Module Gene Set Enrichment Analysis
In csbl-usp/CEMiTool: Co-expression Modules identification Tool

mod_gsea

R Documentation

Module Gene Set Enrichment Analysis

Description

Perfoms Gene Set Enrichment Analysis (GSEA) for each co-expression module found.

Usage

mod_gsea(cem, ...)

## S4 method for signature 'CEMiTool'
mod_gsea(
  cem,
  gsea_scale = TRUE,
  rank_method = "mean",
  gsea_min_size = 15,
  gsea_max_size = 1000,
  verbose = FALSE
)

Arguments

`cem`	Object of class `CEMiTool`.
`...`	Optional parameters.
`gsea_scale`	If TRUE, transform data using z-score transformation. Default: TRUE
`rank_method`	Character string indicating how to rank genes. Either "mean" (the default) or "median".
`gsea_min_size`	Minimum gene set size (Default: 15).
`gsea_max_size`	Maximum gene set size (Default: 1000).
`verbose`	logical. Report analysis steps.

Value

GSEA results.

Examples

# Get example CEMiTool object
data(cem)
# Look at example annotation file
sample_annotation(cem)
# Run GSEA on network modules
cem <- mod_gsea(cem)
# Check results
gsea_data(cem)

csbl-usp/CEMiTool documentation built on March 27, 2024, 5:14 a.m.