fun_enrich: Performs appropriate enrichment on given sets of proteins or...

In nicohuttmann/pOmics: Framework for proteomics data analysis

Performs appropriate enrichment on given sets of proteins or values

Description

Performs appropriate enrichment on given sets of proteins or values

Usage

fun_enrich(
  proteins,
  background = NULL,
  database = "GO",
  pvalueCutoff = 0.05,
  pAdjustMethod = "none",
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500,
  inverse = F,
  dataset,
  view = T
)

Arguments

proteins	list of proteins/scores/protein groups
background	(optional) background genes
database	database(s) to use
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
inverse	scores: enriches for higher scores if TRUE
dataset	dataset
view	View results
threshold	p-value/confidence threshold to exclude terms

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