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R
DOSE

GSEA_internal

GSEA_internal

Description

generic function for gene set enrichment analysis

Usage

GSEA_internal(
  geneList,
  exponent,
  minGSSize,
  maxGSSize,
  eps,
  pvalueCutoff,
  pAdjustMethod,
  verbose,
  seed = FALSE,
  USER_DATA,
  by = "fgsea",
  ...
)

Arguments

geneList

order ranked geneList
exponent

weight of each step
minGSSize

minimal size of each geneSet for analyzing
maxGSSize

maximal size of each geneSet for analyzing
eps

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

p value Cutoff
pAdjustMethod

p value adjustment method
verbose

print message or not
seed

set seed inside the function to make result reproducible. FALSE by default.
USER_DATA

annotation data
by

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

other parameter

Value

gseaResult object

Author(s)

Yu Guangchuang

DOSE

Disease Ontology Semantic and Enrichment analysis

v3.16.0
Artistic-2.0
Authors
Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb], Erqiang Hu [ctb]
Initial release

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