R: Maps between manufacturer IDs and Gene Ontology (GO) IDs
m10kcodGO
R Documentation
Maps between manufacturer IDs and Gene Ontology (GO) IDs
Description
m10kcodGO 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
(m10kcodGO2PROBE) do NOT associate the child terms from the GO
ontology with the gene. Only the directly evidenced terms are
represented here.
m10kcodGO2ALLPROBES 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
m10kcodGO2PROBE.
Details
If m10kcodGO 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:
If m10kcodGO2ALLPROBES or m10kcodGO2PROBE 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: 20150919
x <- m10kcodGO
# 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(m10kcodGO2PROBE)
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 m10kcodGO2ALLPROBES to a list
xx <- as.list(m10kcodGO2ALLPROBES)
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]])
}