aa2selfscore: aa2selfscore
In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
aa2selfscore R Documentation
aa2selfscore
Description
This function return the selfscore from an AAStringSet.
Usage
aa2selfscore(aa, scorematrix = "BLOSUM62")
Arguments
aa
AAStringSet [mandatory]
scorematrix
score matrix to use [default: BLOSUM62]
Value
data.frame
Author(s)
Kristian K Ullrich
See Also
XStringSet-class,
substitution_matrices
Examples
data(woodmouse, package="ape")
#cds2aa(dnabin2dnastring(woodmouse), shorten=TRUE,
#genetic.code=Biostrings::getGeneticCode("2"))
woodmouse |> dnabin2dnastring() |> cds2aa(shorten=TRUE,
genetic.code=Biostrings::getGeneticCode("2")) |> aa2selfscore()
kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.
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| aa2selfscore | R Documentation |
aa2selfscore
Description
This function return the selfscore from an AAStringSet.
Usage
aa2selfscore(aa, scorematrix = "BLOSUM62")
Arguments
aa |
|
scorematrix |
score matrix to use [default: BLOSUM62] |
Value
data.frame
Author(s)
Kristian K Ullrich
See Also
XStringSet-class,
substitution_matrices
Examples
data(woodmouse, package="ape")
#cds2aa(dnabin2dnastring(woodmouse), shorten=TRUE,
#genetic.code=Biostrings::getGeneticCode("2"))
woodmouse |> dnabin2dnastring() |> cds2aa(shorten=TRUE,
genetic.code=Biostrings::getGeneticCode("2")) |> aa2selfscore()
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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