lumiRatAllGO {lumiRatAll.db} | R Documentation

## Map between Manufacturer IDs and Gene Ontology (GO)

### Description

lumiRatAllGO is an R object that provides mappings between manufacturer identifiers and the GO identifiers that they are directly associated with.

### Details

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

### Examples

            x <- lumiRatAllGO
            # 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"]]

            }

[Package lumiRatAll.db version 1.2.0 Index]