dnastring2aln: dnastring2aln
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
View source: R/dnastring2aln.R
Description
This function converts a DNAStringSet into an
seqinr alignment.
Usage
1
dnastring2aln(dna)
Arguments
dna
DNAStringSet [mandatory]
Value
An object of class alignment which is a list with the
following components:
nb the number of aligned sequences
nam a vector of strings containing the names of the aligned
sequences
seq a vector of strings containing the aligned sequences
com a vector of strings containing the commentaries for each sequence
or NA if there are no comments
Author(s)
Kristian K Ullrich
See Also
Examples
1
2
3
4
5
6
7
8
## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATG---CATTGC")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
Biostrings::DNAStringSet(cds2))
## convert into alignment
#dnastring2aln(cds1.cds2.aln)
cds1.cds2.aln |> dnastring2aln()
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
View source: R/dnastring2aln.R
Description
This function converts a DNAStringSet into an
seqinr alignment.
Usage
1 | dnastring2aln(dna)
|
Arguments
dna |
|
Value
An object of class alignment which is a list with the
following components:
nb the number of aligned sequences
nam a vector of strings containing the names of the aligned
sequences
seq a vector of strings containing the aligned sequences
com a vector of strings containing the commentaries for each sequence
or NA if there are no comments
Author(s)
Kristian K Ullrich
See Also
Examples
1 2 3 4 5 6 7 8 | ## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATG---CATTGC")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
Biostrings::DNAStringSet(cds2))
## convert into alignment
#dnastring2aln(cds1.cds2.aln)
cds1.cds2.aln |> dnastring2aln()
|
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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