calcICs: Calculate information contents of GO terms.
In GOSim: Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Description
Usage
Arguments
Details
Value
See Also
Examples
View source: R/termSimilarity.R
Description
Recalculates the information content of all GO terms.
Usage
1
calcICs(DIR=".")
Arguments
DIR
directory where to put the resulting files
Details
This functions should only be invoked, if one wants to calculate the
information content for GO terms with respect to combinations of
evidence codes other than the precomputed ones or, if a
new version of the organism annotation packages has been installed.
By default the information contents are precomputed using all
evidence codes and evidence codes "IMP, IGI, IDA, IEP, IPI" together.
Value
Puts a file named "ICs<ontology><organism><evidence levels>.rda" in
directoy DIR. It can be used afterwards by calling setOntology.
See Also
Examples
1
2
3
4
5
6
setEvidenceLevel("IMP")
setOntology("CC", loadIC=FALSE) # important: setOntology assumes that the IC file already exists. To prevent an error message we need the second argument
calcICs()
# --> this may take some time ...
GOSim documentation built on Nov. 8, 2020, 11:05 p.m.
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Description Usage Arguments Details Value See Also Examples
View source: R/termSimilarity.R
Description
Recalculates the information content of all GO terms.
Usage
1 | calcICs(DIR=".")
|
Arguments
DIR |
directory where to put the resulting files |
Details
This functions should only be invoked, if one wants to calculate the information content for GO terms with respect to combinations of evidence codes other than the precomputed ones or, if a new version of the organism annotation packages has been installed. By default the information contents are precomputed using all evidence codes and evidence codes "IMP, IGI, IDA, IEP, IPI" together.
Value
Puts a file named "ICs<ontology><organism><evidence levels>.rda" in
directoy DIR. It can be used afterwards by calling setOntology.
See Also
Examples
1 2 3 4 5 6 |
setEvidenceLevel("IMP")
setOntology("CC", loadIC=FALSE) # important: setOntology assumes that the IC file already exists. To prevent an error message we need the second argument
calcICs()
# --> this may take some time ...
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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