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Last data update: 2014.03.03

R: Maps between manufacturer IDs and Gene Ontology (GO) IDs

illuminaMousev2GO

R Documentation

Maps between manufacturer IDs and Gene Ontology (GO) IDs

Description

illuminaMousev2GO is an R object that provides mappings between manufacturer identifiers and the GO identifiers that they are directly associated with. This mapping and its reverse mapping (illuminaMousev2GO2PROBE) do NOT associate the child terms from the GO ontology with the gene. Only the directly evidenced terms are represented here.

illuminaMousev2GO2ALLPROBES is an R object that provides mappings between a given GO identifier and all of the manufacturer identifiers annotated at that GO term OR TO ONE OF IT'S CHILD NODES in the GO ontology. Thus, this mapping is much larger and more inclusive than illuminaMousev2GO2PROBE.

Details

If illuminaMousev2GO is cast as a list, each manufacturer 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 manufacturer id. Some of 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

A more complete listing of evidence codes can be found at:

http://www.geneontology.org/GO.evidence.shtml

If illuminaMousev2GO2ALLPROBES or illuminaMousev2GO2PROBE is cast as a list, each GO term maps to a named vector of manufacturer identifiers and evidence codes. A GO identifier may be mapped to the same manufacturer identifier more than once but the evidence code can be different. Mappings between Gene Ontology identifiers and Gene Ontology terms and other information are available in a separate data package named GO.

Whenever any of these mappings are cast as a data.frame, all the results will be output in an appropriate tabular form.

Mappings between manufacturer identifiers and GO information were obtained through their mappings to manufacturer identifiers. NAs are assigned to manufacturer 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.

All mappings were based on data provided by: Gene Ontology ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ With a date stamp from the source of: 20150314

References

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

Examples

    x <- illuminaMousev2GO
    # Get the manufacturer identifiers that are mapped to a GO ID
    mapped_genes <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_genes])
    if(length(xx) > 0) {
        # Try the first one
        got <- xx[[1]]           
        got[[1]][["GOID"]]
        got[[1]][["Ontology"]]
        got[[1]][["Evidence"]]
    }
    # For the reverse map:
    # Convert to a list
    xx <- as.list(illuminaMousev2GO2PROBE)
    if(length(xx) > 0){
        # Gets the manufacturer ids for the top 2nd and 3nd GO identifiers
        goids <- xx[2:3]
        # Gets the manufacturer ids for the first element of goids
        goids[[1]]
        # Evidence code for the mappings
        names(goids[[1]])
    }
    # Convert illuminaMousev2GO2ALLPROBES to a list
    xx <- as.list(illuminaMousev2GO2ALLPROBES)
    if(length(xx) > 0){
        # Gets the manufacturer identifiers for the top 2nd and 3nd GO identifiers
        goids <- xx[2:3]
        # Gets all the manufacturer identifiers for the first element of goids
        goids[[1]]
        # Evidence code for the mappings
        names(goids[[1]])
    }

Results