topGO {limma} | R Documentation

## Table of Top GO Terms or Top KEGG Pathways

### Description

Extract top GO terms from goana output or top KEGG pathways from kegga output.

### Usage

    topGO(results, ontology = c("BP", "CC", "MF"), sort = NULL, number = 20L,
          truncate.term = NULL)
    topKEGG(results, sort = NULL, number = 20L, truncate.path = NULL)

### Arguments

`results` | data frame produced by `goana` or `kegga`.
`ontology` | character vector of ontologies to be included in output. Elements should be one or more of `"BP"`, `"CC"` or `"MF"`.
`sort` | character vector of names of gene lists for which results are required. Should be one or more of the column names of `results`. Defaults to all gene lists.
`number` | maximum number of top GO terms or top KEGG pathways to list. For all terms or all pathways, set `number=Inf`.
`truncate.term` | truncate the name of the GO term at this number of characters.
`truncate.path` | truncate the name of the KEGG pathway at this number of characters.

### Details

`topGO` organizes the output from `goana` into top-tables of the most significant GO terms. `topKEGG` similarly extracts the most significant KEGG pathways from `kegga` output. In either case, rows are sorted by the minimum p-value of any of the result columns specified by `sort`.

### Value

Same as `results` but with rows subsetted by Ontology and sorted by p-value.

### Author(s)

Gordon Smyth and Yifang Hu

### See Also

`goana`, `kegga`

See 10.GeneSetTests for a description of other functions used for gene set testing.

### Examples

    # See goana examples

[Package limma version 3.38.3 Index]