topGO: Table of Top GO Terms or Top KEGG Pathways
In hdeberg/limma: Linear Models for Microarray Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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.

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.

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

Gordon Smyth and Yifang Hu

goana, kegga

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