setEvidenceLevel {GOSim}R Documentation

Specifies to use only GO terms with given evidence codes.

Description

Specifies to use only GO terms with given evidence codes.

Usage

setEvidenceLevel(evidences = "all")

Arguments

evidences character vector of evidence codes

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

Mappings were based on data provided by:

Entrez Gene: <URL: http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/>. Built: Source data downloaded from Entrez Gene on Fri Sep 30 02:51:32 2005

Value

none.

Note

The method directly uses the "GO" library to obtain the mappings of the Entrez Gene IDs to GO terms. Internally this mapping is especially used for calculating the information content of the GO terms. By default all evidence codes are used for this. If another behavior is wanted, one has to recalculate the information content of all GO terms via calcICs. The evidence level also influences the behavior of filterGO and getGOInfo.

Author(s)

Holger Froehlich

References

<URL: http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene>

See Also

calcICs, filterGO, getGOInfo

Examples

        ## Not run: setEvidenceLevel("all") # the default behavior        

[Package GOSim version 1.1.3.2 Index]