do_ORA: Performs overexpression enrichment on logical protein vector...

In nicohuttmann/pOmics: Framework for proteomics data analysis

Performs overexpression enrichment on logical protein vector with specified Ontology

Description

Performs overexpression enrichment on logical protein vector with specified Ontology

Usage

do_ORA(
  proteins,
  database,
  pvalueCutoff = 0.05,
  pAdjustMethod = "none",
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500,
  algorithm = "classic",
  dataset
)

Arguments

proteins	character vector
database	database to use
pvalueCutoff	p-value/confidence threshold to exclude terms
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

nicohuttmann/pOmics documentation built on Sept. 21, 2022, 9:28 a.m.