GeneAnswers (version 2.14.0)

topREACTOME.PATHGenes: Present top REACTOME.PATH enrichment test information with genes

Description

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

Usage

topREACTOME.PATHGenes(x, catTerm = TRUE, keepID=TRUE, geneSymbol = TRUE, ...)

Arguments

x

a given GeneAnswers instance with REACTOME.PATH test

catTerm

logic value to determine whether mapping REACTOME.PATH IDs to REACTOME.PATH terms

keepID

logic, to determine whether keep REACTOME.PATH 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

topCategoryGenes

Examples

##x is a GeneAnswers instance with REACTOME.PATH test
## Not run: topREACTOME.PATHGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE)