geneAnswersReadable: Make GeneAnswers Instance readable

In GeneAnswers: Integrated Interpretation of Genes

Description

a function to mapping category IDs and gene IDs to names and symbols.

Usage

geneAnswersReadable(x, catTerm = TRUE, geneSymbol = TRUE, strict = FALSE, verbose=TRUE, missing=c('name', 'keep', 'remove'), ...)

Arguments

x	a GeneAnswers instance containing category IDs and geneIDs
catTerm	logic value to determine whether mapping category IDs to names
geneSymbol	logic value to determine whether mapping gene IDs to symbols
strict	logic value to determine whether interrupt conversion if NA is introduced.
verbose	logical, show current stage or not
missing	type of handling NA mapping.
...	other parameters used by getCategoryTerms

Details

Conversion could stop if NA is introduced and strict is set to TRUE. 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. Occationally, Reactome uses the same name for species-mixed pathways based on in vivo and in vitro experiments, so we highly recommend to set addID as TRUE for Reactome test.

Value

return a GeneAnswers instance with category names and/or gene symbols.

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

getSymbols, getCategoryTerms

Examples

example(GeneAnswers)
xx <- geneAnswersReadable(x) 

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