getCategoryTerms: Mapping Category IDs to Terms

In GeneAnswers: Integrated Interpretation of Genes

Description

Function to map category IDs to category terms.

Usage

getCategoryTerms(catIDs, catType, strict = FALSE, missing=c('name', 'keep', 'remove'), nameLength='all', addID=FALSE)

Arguments

catIDs	a character vector containing category IDs
catType	type of category
strict	logic value to stop conversion if NA is introduced.
missing	type of handling NA mapping.
nameLength	show how many first letters for long term names, 'all' for full name
addID	logic, add term IDs following term names or not

Details

The current version only supports 'GO', 'DOLITE', 'KEGG', 'REACTOME.PATH' and 'CABIO.PATH'. There are three types of parameters for variable 'missing'. 'name' means the NA mapping values are replaced by their names. 'keep' means all of NA values are kept. 'remove' means all of NA values are removed.

Value

return category terms of given category IDs.

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

getCategoryTerms(c("04640", "05221", "05215"), catType='KEGG')

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