getAllGOlists: getAllGOlists

In plger/clustView: clustView

Description

Returned as list of genes for each GO term

Usage

getAllGOlists(species = "Mm", translate.cat.ids = TRUE,
  gene.id.type = "symbol", genes = NULL, minSize = 10,
  maxSize = 500, returnGeneSets = FALSE, categories = NULL,
  ontologies = c("BP", "CC", "MF"))

Arguments

species	Two-letter species code (corresponding to the 'org.Xx.eg' package)
translate.cat.ids	Logical; whether to translate GO category IDs to terms
gene.id.type	The type of gene identifier to return; either 'symbol' (default) or 'ensembl'.
genes	The subset of genes to use.
minSize	The minimum set size (default 10).
maxSize	The maximum set size (default 500).
returnGeneSets	Logical; whether to return an object of class 'GeneSetCollection' rather than a normal list (default FALSE).
categories	The GO categories to use (default all)
ontologies	The GO tree to use; any combination of "BP", "CC", and "MF" (default all)

Value

A named list of genes, or a 'GeneSetCollection' if 'returnGeneSets=T'

plger/clustView documentation built on May 31, 2019, 5:42 a.m.