gsea: Gene Set Enrichment Analysis

In RGLab/HIPCMatrix: Microarray and RNA-seq Processing for ImmuneSpace

Gene Set Enrichment Analysis

Description

Perform a gene set enrichment analysis on an expressionset using the CAMERA method.

Usage

gsea(
  eset,
  set_name = "msigdb",
  gene_sets = NULL,
  contrast = "study_time_collected",
  baseline = NULL
)

Arguments

eset	expressionset
set_name	Name of predefined set of gene signatures. Choose from: chaussabel, blood_transcription, msigdb
gene_sets	A list of vectors of gene names, each entry corresponding to a gene set. If specified, this will be used in place of the "set_name" argument to test gene sets.
contrast	contrast
baseline	Value to compare other contrast values against. By default, uses first when coerced to factor.

RGLab/HIPCMatrix documentation built on Jan. 29, 2023, 5:13 a.m.