do_ORA_Reactome: Performs over-representation analysis using Reactome...
In nicohuttmann/pOmics: Framework for proteomics data analysis

do_ORA_Reactome

R Documentation

Performs over-representation analysis using Reactome annotations

Description

Performs over-representation analysis using Reactome annotations

Usage

do_ORA_Reactome(
  proteins,
  pvalueCutoff = 0.05,
  pAdjustMethod = "none",
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500,
  dataset,
  view = F,
  return.all = F,
  add.info = F
)

Arguments

`proteins`	numeric/logical vector of proteins indicating group
`pvalueCutoff`	p-value cutoff for annotations
`pAdjustMethod`	one of "none", "BH" (Benjamini-Hochberg correction), "hochberg", "bonferroni", "holm", "hommel", "BY", "fdr"
`qvalueCutoff`	q-value cutoff for annotations
`minGSSize`	minimum number of annotated proteins to be included
`maxGSSize`	maximum number of annotated proteins to be included
`dataset`	dataset
`view`	view results
`return.all`	return enrichResult object; useful for further analysis of enrichment results
`add.info`	add additional information to the results data frame