R: Topic: Gene Set Tests

10.GeneSetTests {limma}

R Documentation

Topic: Gene Set Tests

This page gives an overview of the LIMMA functions for gene set testing and pathway analysis.

roast: Self-contained gene set testing for one set.
mroast: Self-contained gene set testing for many sets.
fry: Fast approximation to mroast, especially useful when heteroscedasticity of genes can be ignored.
camera: Competitive gene set testing.
romer and topRomer: Gene set enrichment analysis.
ids2indices: Convert gene sets consisting of vectors of gene identifiers into a list of indices suitable for use in the above functions.
alias2Symbol and alias2SymbolTable: Convert gene symbols or aliases to current official symbols.
geneSetTest or wilcoxGST: Simple gene set testing based on gene or probe permutation.
barcodeplot: Enrichment plot of a gene set.
goana and topGO: Gene ontology over-representation analysis of gene lists using Entrez Gene IDs. goana can work directly on a fitted model object or on one or more lists of genes.
kegga and topKEGG: KEGG pathway over-representation analysis of gene lists using Entrez Gene IDs. kegga can work directly on a fitted model object or on one or more lists of genes.

Gordon Smyth