GSEA_internal: GSEA_internal

View source: R/gsea.R

GSEA_internalR Documentation

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


YuLab-SMU/DOSE documentation built on Nov. 3, 2024, 9:37 p.m.