do_GSEA: Performs gene set enrichment on numeric protein vector with...

In nicohuttmann/pOmics: Framework for proteomics data analysis

Performs gene set enrichment on numeric protein vector with specified Ontology

Description

Performs gene set enrichment on numeric protein vector with specified Ontology

Usage

do_GSEA(
  proteins,
  database,
  inverse = F,
  pvalueCutoff = 0.05,
  pAdjustMethod = "none",
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 120,
  dataset,
  return.all = F,
  add.info = F
)

Arguments

proteins	numeric score vector
database	database to use
inverse	enrich for terms in higher values/scores
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
return.all	Should the enrichrObject be returned
add.info	Add additional information (takes longer)

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