geneSetOpts: geneSetOpts

In PavlidisLab/ermineR: Gene set analysis with multifunctionality assessment

geneSetOpts

Description

geneSetOpts

Usage

geneSetOpts(
  geneSetDescription = "Latest_GO",
  customGeneSets = NULL,
  minClassSize = 20,
  maxClassSize = 200
)

Arguments

geneSetDescription	"Latest_GO", a file path that leads to a GO XML or OBO file or a URL that leads to a go ontology file that ends with rdf-xml.gz. If you left annotation as NULL and provided customGeneSets, this argument is not required and will default to NULL. Otherwise, by default it'll be set to "Latest_GO" which downloads the latest available GO XML file. This option won't work without an internet connection. To get a frozen file that you can use later, see goToday, goAtDate and getGoDates. See http://erminej.msl.ubc.ca/help/input-files/gene-set-descriptions/ for details.
customGeneSets	Path to a directory that contains custom gene set files, paths to custom gene set files themselves or a named list of character strings. Use this option to create your own gene sets. If you provide directory you can specify probes or gene symbols to include in your gene sets. See http://erminej.msl.ubc.ca/help/input-files/gene-sets/ for information about format for this file. If you are providing a list, only gene symbols are accepted.
minClassSize	minimum class size
maxClassSize	maximum class size

PavlidisLab/ermineR documentation built on Sept. 18, 2024, 5:12 a.m.