topCategory {GeneAnswers} | R Documentation

## 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

### 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.

### 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

### Examples

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

[Package GeneAnswers version 2.32.0 Index]