enricher_all: Run enricher from clusterProfiler on all DESeq2 result tables

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Run enricher from clusterProfiler on all DESeq2 result tables

Description

Run enricher from clusterProfiler on all DESeq2 result tables

Usage

enricher_all(
  res,
  gsets,
  maxGSSize = 2000,
  expressed_universe = TRUE,
  deseq.padj = 0.05,
  logFC,
  protein_coding = TRUE,
  quiet = FALSE,
  ...
)

Arguments

res	A list of DESeq results
gsets	A list of gene sets (or two column dataframe with pathway and gene)
maxGSSize	Maximum set size, default 2000
expressed_universe	Use all expressed genes as universe, default TRUE
deseq.padj	Adjusted p-value cutoff for significant genes, default 0.05
logFC	absolute fold change cutoff
protein_coding	compare protein coding genes only, default TRUE
quiet	suppress messages except total significant
...	Additional options like minGSSize and pvalueCutoff passed to enricher

Value

A list of tibbles

Author(s)

Chris Stubben

Examples

## Not run: 
library(hciRdata)
enricher_all(res, msig_pathways$KEGG)

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on March 26, 2024, 3:09 a.m.