pickGO: Cleans up result from org...
In AnnotationFuncs: Annotation translation functions

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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.

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!

List with only the picked elements.

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

pickRefSeq, getEvidenceCodes, translate

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'))