pickGO: Cleans up result from org...

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

View source: R/annotation-funcs.R

Description

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

Usage

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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.

Details

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!

Value

List with only the picked elements.

Author(s)

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

See Also

pickRefSeq, getEvidenceCodes, translate

Examples

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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'))

AnnotationFuncs documentation built on May 31, 2017, 11:01 a.m.

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