10.GeneSetTests {limma} | R Documentation

## Topic: Gene Set Tests

### Description

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. Uses `zscoreT` to normalize t-statistics.

`mroast`

  Self-contained gene set testing for many sets. Uses `zscoreT` to normalize t-statistics.

`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`, `alias2SymbolTable` and `alias2SymbolUsingNCBI`

  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.

### Author(s)

Gordon Smyth

### See Also

01.Introduction, 02.Classes, 03.ReadingData, 04.Background, 05.Normalization, 06.LinearModels, 07.SingleChannel, 08.Tests, 09.Diagnostics, 10.GeneSetTests, 11.RNAseq

[Package limma version 3.42.2 Index]