OperonHumanV3GO {OperonHumanV3.db} | R Documentation |
OperonHumanV3GO is an R object that provides mappings between manufacturer identifiers and the GO identifiers that they are directly associated with.
Each Entrez Gene identifier is mapped to a list of lists. The names on the outer list are GO identifiers. Each inner list consists of three named elements: GOID, Ontology, and Evidence.
The GOID element matches the GO identifier named in the outer list and is included for convenience when processing the data using 'lapply'.
The Ontology element indicates which of the three Gene Ontology categories this identifier belongs to. The categories are biological process (BP), cellular component (CC), and molecular function (MF).
The Evidence element contains a code indicating what kind of evidence supports the association of the GO identifier to the Entrez Gene id. The evidence codes in use include:
IMP: inferred from mutant phenotype
IGI: inferred from genetic interaction
IPI: inferred from physical interaction
ISS: inferred from sequence similarity
IDA: inferred from direct assay
IEP: inferred from expression pattern
IEA: inferred from electronic annotation
TAS: traceable author statement
NAS: non-traceable author statement
ND: no biological data available
IC: inferred by curator
Mappings between probe identifiers and GO information were obtained through their mappings to Entrez Gene identifiers. NAs are assigned to probe identifiers that can not be mapped to any Gene Ontology information. Mappings between Gene Ontology identifiers an Gene Ontology terms and other information are available in a separate data package named GO.
Mappings were based on data provided by: Gene Ontology ( ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest ) on 200803
x <- OperonHumanV3GO # Get the probe identifiers that are mapped to a GO ID mapped_probes <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_probes]) if(length(xx) > 0) { # Try the firest one got <- xx[[1]] got[[1]][["GOID"]] got[[1]][["Ontology"]] got[[1]][["Evidence"]] }