Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!
Get Started for Free

gseGO

gseGO

Description

Gene Set Enrichment Analysis of Gene Ontology

Usage

gseGO(
  geneList,
  ont = "BP",
  OrgDb,
  keyType = "ENTREZID",
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  eps = 1e-10,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  seed = FALSE,
  by = "fgsea",
  ...
)

Arguments

geneList

order ranked geneList
ont

one of "BP", "MF", and "CC" subontologies, or "ALL" for all three.
OrgDb

OrgDb
keyType

keytype of gene
exponent

weight of each step
minGSSize

minimal size of each geneSet for analyzing
maxGSSize

maximal size of genes annotated for testing
eps

This parameter sets the boundary for calculating the p value.
pvalueCutoff

pvalue Cutoff
pAdjustMethod

pvalue adjustment method
verbose

print message or not
seed

logical
by

one of 'fgsea' or 'DOSE'
...

other parameter

Value

gseaResult object

Author(s)

Yu Guangchuang

clusterProfiler

statistical analysis and visualization of functional profiles for genes and gene clusters

v3.18.1
Artistic-2.0
Authors
Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb] (formula interface of compareCluster)
Initial release

We don't support your browser anymore

Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.