| org.At.tairGO {org.At.tair.db} | R Documentation |
org.At.tairGO is an R object that provides mappings between TAIR identifiers and the GO identifiers that they are directly associated with. This mapping and its reverse mapping do NOT associate the child terms from the GO ontology with the gene. Only the directly evidenced terms are represented here.
Each TAIR 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 TAIR Gene 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
Mappings between TAIR gene identifiers and GO information were obtained through their mappings to TAIR gene identifiers. NAs are assigned to TAIR 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-lite/ With a date stamp from the source of: 20130907
For the reverse map GO2TAIR, each GO term maps to a named vector of TAIR gene identifiers. A GO identifier may be mapped to the same TAIR 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.
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
x <- org.At.tairGO
# Get the TAIR gene 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(org.At.tairGO2TAIR)
if(length(xx) > 0){
# Gets the TAIR gene ids for the top 2nd and 3nd GO identifiers
goids <- xx[2:3]
# Gets the TAIR ids for the first element of goids
goids[[1]]
# Evidence code for the mappings
names(goids[[1]])
}