topCategoryGenes: Present top enrichment test information with genes

In GeneAnswers: Integrated Interpretation of Genes

Description

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

Usage

topCategoryGenes(inputX, orderby = c("geneNum", "pvalue", "foldChange", "oddsRatio", "correctedPvalue"), top = 5, genesOrderBy = 1, decreasing = FALSE, topGenes = 5, file = FALSE, fileName = "topCategoryGenes.txt")

Arguments

inputX	a given GeneAnswers instance
orderby	type to sort enrichmentInfo slot
top	integer to specify how many top rows to be presented
genesOrderBy	integer or characters to specify gene ordered column.
decreasing	logic value to specify gene order is descending or not
topGenes	integer to speicify how many top genes to be presented
file	logic value to determine whether save to a file
fileName	string to specify file name, default file name is topCategoryGenes.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. topGenes is similar to top, but only top 5 genes will be displayed for 'ALL'. genesOrderBy could be an integer to specify column to be sorted. It can also be the column name. If set to 'none', no sorting for genes.

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: topCategoryGenes(x, orderby='p')

GeneAnswers documentation built on Nov. 8, 2020, 4:53 p.m.