caBIO.PATHGenes: Present top CABIO.PATH enrichment test information with genes

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

Description

Function to present top CABIO.PATH enichmentInfo of given GeneAnswers instance with genes. This function is not supported starting this version due to the termination of the caBig project.

Usage

1
topcaBIO.PATHGenes(x, catTerm = TRUE, keepID=TRUE, geneSymbol = TRUE, ...)

Arguments

x

a given GeneAnswers instance with CABIO.PATH test

catTerm

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

keepID

logic, to determine whether keep CABIO.PATH 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

topCategoryGenes

Examples

1
2
##x is a GeneAnswers instance with CABIO.PATH test
## Not run: topcaBIO.PATHGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE)

GeneAnswers documentation built on May 20, 2017, 10:09 p.m.

Search within the GeneAnswers package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.