GeneAnswers (version 2.14.0)

topCategory: Present top enrichment test information

Description

Function to present top enichmentInfo of given GeneAnswers instance.

Usage

topCategory(inputX, orderby = c("geneNum", "pvalue", "foldChange", "oddsRatio", "correctedPvalue"), top = 5, file = FALSE, fileName = "topCategory.txt")

Arguments

inputX

a given GeneAnswers instance

orderby

type to sort enrichmentInfo slot

top

integer to specify how many top rows to be presented

file

logic value to determine whether save to a file

fileName

string to specify file name, default file name is topCategory.txt

Value

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

Details

orderby could be one of 'geneNum', 'pvalue', 'foldChange', 'oddsRatio' and 'correctedPvalue'. top could be an integer or 'ALL'. The top former specified categories will be printed on screen while only 30 categories will be displayed for 'ALL'. All categories can be saved in a specified file.

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

Examples

# x is a GeneAnswers instance
## Not run: topCategory(x, orderby='pvalue')

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