pickGO {bioCancer} | R Documentation

## Cleans up result from org.Xx.egGO and returns specific GO identifiers

### Description

Cleans up result from org.Xx.egGO and returns GO identifier for either biological process (BP), cellular component (CC), or molecular function (MF). Can be used on list of GOs from `translate`, or a single list of GOs from an annotation package. May reduce list, if the (sub)list does not contain the chosen class!

### Usage

    pickGO(l, evidence = NA, category = NA)

### Arguments

`l` | Character vector, or list of, og GO identifiers.
`evidence` | Character vector, filters on which kind of evidence to return; for a larger list see `getEvidenceCodes`. \* Evidence codes may be: `c('IMP','IGI','IPI','ISS','IDA','IEP','IEA','TAS','NAS','ND','IC')`. \* Leave as `NA` to ignore filtering on this part.
`category` | Character vector, filters on which ontology to return: biological process (BP), cellular component (CC), or molecular function (MF). \* Leave as `NA` to ignore filtering on this part.

### Value

List with only the picked elements.

### Author(s)

Stefan McKinnon Edwards stefan.hoj-edwards@agrsci.dk

### See Also

`pickRefSeq`, `getEvidenceCodes`, `translate`

### Examples

    library(org.Bt.eg.db)
    genes <- c(280705, 280706, 100327208)
    GO <- translate(genes, org.Bt.egGO)
    # Get all biological processes:
    pickGO(GO, category='BP')
    # Get all ontologies with experimental evidence:
    pickGO(GO, evidence=c('IMP','IGI','IPI','ISS','IDA','IEP','IEA'))

[Package bioCancer version 1.20.02 Index]