topPATHGenes {GeneAnswers} | R Documentation

## Present top KEGG enrichment test information with genes

### Description

Function to present top KEGG enichmentInfo of given GeneAnswers instance with genes.

### Usage

    topPATHGenes(x, catTerm = TRUE, keepID=TRUE, geneSymbol = TRUE, ...)

### Arguments

`x` | a given GeneAnswers instance with KEGG test
`catTerm` | logic value to determine whether mapping KEGG IDs to KEGG terms
`keepID` | logic, to determine whether keep KEGG IDs
`geneSymbol` | logic value to determine whether mapping gene Entrez IDs to gene symbols
`...` | other parameters to transfer to topCategoryGenes

### Details

See function topCategoryGenes help for details

### Value

print necessary information on the screen and save into a specified file if request.

### Author(s)

Gang Feng, Pan Du and Simon Lin

### References

Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10

### See Also

~~objects to See Also as `topCategoryGenes`, ~~~

### Examples

    ##x is a GeneAnswers instance with KEGG test
    ## Not run: topPATHGenes(x, geneSymbol=TRUE, orderby='genenum', top=6, topGenes=8, genesOrderBy='foldChange')

[Package GeneAnswers version 2.22.0 Index]