aln2aastring: aln2aastring
In kullrich/distSTRING: distSTRING calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
Description
This function converts a seqinr alignment into
an AAStringSet.
Usage
1
aln2aastring(aln)
Arguments
aln
seqinr alignment [mandatory]
Value
An object of class AAStringSet
Author(s)
Kristian K Ullrich
See Also
Examples
1
2
3
4
5
6
7
## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATG---CATTGC")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
Biostrings::DNAStringSet(cds2))
#aastring2aln(cds2aa(cds1.cds2.aln))
cds1.cds2.aln |> cds2aa() |> aastring2aln() |> aln2aastring()
kullrich/distSTRING documentation built on Dec. 21, 2021, 8:42 a.m.
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Description Usage Arguments Value Author(s) See Also Examples
Description
This function converts a seqinr alignment into
an AAStringSet.
Usage
1 | aln2aastring(aln)
|
Arguments
aln |
|
Value
An object of class AAStringSet
Author(s)
Kristian K Ullrich
See Also
Examples
1 2 3 4 5 6 7 | ## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATG---CATTGC")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
Biostrings::DNAStringSet(cds2))
#aastring2aln(cds2aa(cds1.cds2.aln))
cds1.cds2.aln |> cds2aa() |> aastring2aln() |> aln2aastring()
|
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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