geneAnswersReadable {GeneAnswers} | R Documentation

## Make GeneAnswers Instance readable

### 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)

[Package GeneAnswers version 2.22.0 Index]