seekGSEA: GSEA for GO terms

In Solatar/seeqR:

Description

Imports: fgsea, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GO.db

Usage

seekGSEA(
  rankedList,
  Species = NA,
  genesetList = "GO",
  Ont = "BP",
  output_IDs = "SYMBOL",
  minSize = 5,
  maxSize = Inf,
  nperm = 1000
)

Arguments

rankedList	vector sorted from high to low values of the ranking metric (e.g. log2 fold change), with entrezids as names.
Species	string, either "human" or "mouse". Is used to retreive the right Entrez IDs for the GO pathways
genesetList	either the string "GO", or a list of genesets of Entrez IDs, all the same Species as the rankedList!
Ont	string, an ontology category: "BP", "CC" or "MF". Not used for custom genesetLists.
output_IDs	string, ID type to be returned for the table (e.g.: "SYMBOL","ENTREZID","ENSEMBL",...)
minSize	Minimal size of a gene set to test. All pathways below the threshold are excluded.
maxSize	Maximal size of a gene set to test. All pathways above the threshold are excluded.
nperm	Number of permutations to do. Minimial possible nominal p-value is about 1/nperm

Value

data.frame where each row is a GO term, and each column is a parameter of information about the term (e.g. ID, p value, etc.).

Examples

myDE <- sqDE
rl <- seekGSErl(myDE, pFilter=0.05, colentrez="EntrezId")
mygsea <- seekGSEA(rl, Species="mouse", Ont="BP")

Solatar/seeqR documentation built on Feb. 19, 2021, 8:07 p.m.