orfSimilarity: calculate percentage of orfB contained in orfA
In GeneStructureTools: Tools for spliced gene structure manipulation and analysis
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
View source: R/compareTranscripts.R
Description
calculate percentage of orfB contained in orfA
Usage
1
orfSimilarity(orfA, orfB, substitutionCost = 100)
Arguments
orfA
character string of ORF amino acid sequence
orfB
character string of ORF amino acid sequence
substitutionCost
cost for substitutions in ORF sequences.
Set to 1 if substitutions should be weighted equally to insertions and deletions.
Value
percentage of orfB contained in orfA
Author(s)
Beth Signal
See Also
Other ORF annotation: getOrfs,
getUOrfs, maxLocation
Examples
1
2
3
4
5
orfSimilarity("MFGLDIYAGTRSSFRQFSLT","MFGLDIYAGTRSSFRQFSLT")
orfSimilarity("MFGLDIYAGTRSSFRQFSLT","MFGLDIYAFRQFSLT")
orfSimilarity("MFGLDIYAFRQFSLT","MFGLDIYAGTRSSFRQFSLT")
orfSimilarity("MFGLDIYAGTRXXFRQFSLT","MFGLDIYAGTRSSFRQFSLT")
orfSimilarity("MFGLDIYAGTRXXFSLT","MFGLDIYAGTRSSFRQFSLT", 1)
GeneStructureTools documentation built on Nov. 8, 2020, 6:04 p.m.
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Description Usage Arguments Value Author(s) See Also Examples
View source: R/compareTranscripts.R
Description
calculate percentage of orfB contained in orfA
Usage
1 | orfSimilarity(orfA, orfB, substitutionCost = 100)
|
Arguments
orfA |
character string of ORF amino acid sequence |
orfB |
character string of ORF amino acid sequence |
substitutionCost |
cost for substitutions in ORF sequences. Set to 1 if substitutions should be weighted equally to insertions and deletions. |
Value
percentage of orfB contained in orfA
Author(s)
Beth Signal
See Also
Other ORF annotation: getOrfs,
getUOrfs, maxLocation
Examples
1 2 3 4 5 | orfSimilarity("MFGLDIYAGTRSSFRQFSLT","MFGLDIYAGTRSSFRQFSLT")
orfSimilarity("MFGLDIYAGTRSSFRQFSLT","MFGLDIYAFRQFSLT")
orfSimilarity("MFGLDIYAFRQFSLT","MFGLDIYAGTRSSFRQFSLT")
orfSimilarity("MFGLDIYAGTRXXFRQFSLT","MFGLDIYAGTRSSFRQFSLT")
orfSimilarity("MFGLDIYAGTRXXFSLT","MFGLDIYAGTRSSFRQFSLT", 1)
|
R Package Documentation
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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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