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

In kmezhoud/bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

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 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 [e-mail]

See Also

pickRefSeq, getEvidenceCodes, translate

Examples

library(org.Bt.eg.db)
genes <- c(280705, 280706, 100327208)
translate(genes, org.Bt.egSYMBOL)

symbols <- c("SERPINA1","KERA","CD5")
refseq <- translate(symbols, from=org.Bt.egSYMBOL2EG, to=org.Bt.egREFSEQ)
# Pick the proteins:
pickRefSeq(refseq, priorities=c('NP','XP'), reduce='all')

# If you wanted do do some further mapping on the result from
# translate, simply use lapply.

library(GO.db)
GO <- translate(genes, org.Bt.egGO)
# Get all biological processes:
## Not run: 
pickGO(GO, category='BP')
 # $`280705`
 # [1] "GO:0006826" "GO:0006879"
 # $`280706`
# [1] "GO:0006590" "GO:0007165" "GO:0042446"
# Get all ontologies with experimental evidence:
pickGO(GO, evidence=c('IMP','IGI','IPI','ISS','IDA','IEP','IEA'))
 # $`280705`
 # [1] "GO:0006826" "GO:0006879" "GO:0005615" "GO:0008199"
 # $`280706`
 # [1] "GO:0006590" "GO:0007165" "GO:0042446" "GO:0005615" "GO:0005179" "GO:0042393"

## End(Not run)

kmezhoud/bioCancer documentation built on Feb. 17, 2024, 10:29 a.m.