GeneAnswers (version 2.14.0)

topPATHGenes: 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

Value

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

Details

See function topCategoryGenes help for details

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')