gsePathway: gsePathway

Description Usage Arguments Value Author(s)

View source: R/gseAnalyzer.R

Description

Gene Set Enrichment Analysis of Reactome Pathway

Usage

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gsePathway(
  geneList,
  organism = "human",
  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

organism

organism

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

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


ReactomePA documentation built on Nov. 8, 2020, 5:40 p.m.