chickenGO2PROBE {chicken.db} | R Documentation

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

### Description

chickenGO2PROBE is an R object that provides mappings between GO identifiers and manufacturer identifiers.

### Details

Each GO term maps to a named vector of manufacturer identifiers. The name associated with each manufacturer identifier corresponds to the evidence code for that GO identifier. The evidence code indicates what kind of evidence supports the association between the GO and Entrez Gene identifiers. Evidence codes currently 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

A GO identifier may be mapped to the same probe identifier more than once but the evidence code can be different. 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:

Entrez Gene ( ftp://ftp.ncbi.nlm.nih.gov/gene/DATA ) on 2009-Mar11

### References

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

### Examples

        # Convert to a list
        xx <- as.list(chickenGO2PROBE)
        if(length(xx) > 0){
            # Get the probe identifiers for the top 2nd and 3nd GO identifiers
            goids <- xx[2:3]
            # Get the probe identifiers for the first element of goids
            goids[[1]]
            # Evidence code for the mappings
            names(goids[[1]])
        }

[Package chicken.db version 2.2.11 Index]