setEvidenceLevel {GOSim} | R Documentation |
Specifies to use only GO terms with given evidence codes. This, in combination with the specified GO ontology ("BP", "MF", "CC"), influences, how the information content for individual GO terms is calculated.
setEvidenceLevel(evidences = "all", organism=org.Hs.egORGANISM, gomap=org.Hs.egGO)
evidences |
character vector of evidence codes |
organism |
organism, for which to load a mapping of Entrez gene IDs to GO terms (see details) |
gomap |
mapping of Entrez gene IDs to GO terms to be used (see details) |
Each evidence code can be one of:
Entrez Gene ids for which no GO associations exist are left out of the environment.
The method retrieves a mapping of Entrez gene IDs to GO terms, restricted by the given evidence codes. This mapping is based on the respective organism annotation packages (e.g. org.Dm.eg.db for fly, org.Hs.eg.db for human, etc.). The user passes the GO mapping and the organism name to the function. Please refer to the annotation packages for further information.
In case there does not exist an annotation package so far, the user can optionally provide its own mapping of Entrez gene IDs to GO terms instead of using one of the packages mentioned before. The mapping should come in form of a nested list having a format as in the following example (no NAs are allowed):
$`11305`
$`11305`$`GO:0006810`
$`11305`$`GO:0006810`$GOID [1] "GO:0006810"
$`11305`$`GO:0006810`$Evidence [1] "IEA"
$`11305`$`GO:0006810`$Ontology [1] "BP"
$`11305`$`GO:0008203`
$`11305`$`GO:0008203`$GOID
[1] "GO:0008203"
$`11305`$`GO:0008203`$Evidence [1] "ISS"
$`11305`$`GO:0008203`$Ontology [1] "BP"
$`11306`
$`11306`$`GO:0006810`
$`11306`$`GO:0006810`$GOID [1] "GO:0006810"
$`11306`$`GO:0006810`$Evidence [1] "IEA"
$`11306`$`GO:0006810`$Ontology [1] "BP"
$`11306`$`GO:0006879`
$`11306`$`GO:0006879`$GOID
[1] "GO:0006879"
$`11306`$`GO:0006879`$Evidence [1] "IMP"
$`11306`$`GO:0006879`$Ontology [1] "BP"
The mapping is stored in the GOSimEnv environment.
By default all evidence codes are used. If another
behavior is wanted, one has to recalculate the information content of
all GO terms via calcICs
.
The evidence level influences the behavior of all other functions, especially
filterGO
and getGOInfo
.
Holger Froehlich
<www.geneontology.org>
setOntology
, calcICs
, filterGO
, getGOInfo
## Not run: setEvidenceLevel("all") # the default behavior