setEvidenceLevel: Specifies to use only GO terms with given evidence codes.

In GOSim: Computation of functional similarities between GO terms and gene products; GO enrichment analysis

Description

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.

Usage

setEvidenceLevel(evidences = "all", organism=org.Hs.egORGANISM, gomap=org.Hs.egGO)

Arguments

evidences	character vector of evidence codes
organism	organism, for which to load a mapping of primary gene IDs to GO terms (see details)
gomap	mapping of primary gene IDs to GO terms to be used (see details)

Details

Each evidence code can be one of:

"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

Gene ids for which no GO associations exist are left out of the environment.

The method retrieves a mapping of primary gene IDs (usually Entrez) 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 primary 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"

Value

The mapping is stored in the GOSimEnv environment.

Note

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.

Author(s)

Holger Froehlich

References

<www.geneontology.org>

See Also

setOntology, calcICs, filterGO, getGOInfo

Examples

	
	setEvidenceLevel("all")
	 # the default behavior	

GOSim documentation built on Nov. 8, 2020, 11:05 p.m.