DottedAlignment: Align haplotypes into a dotted alignment
In QSutils: Quasispecies Diversity
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
View source: R/DottedAlignment.R
Description
Given an alignment, it takes the first sequence as reference, and depicts
all equivalences in the alignment as dots, leaving only the variants with
respect to the reference.
Usage
1
DottedAlignment(hseqs)
Arguments
hseqs
DNAStringSet or AAStringSet with haplotype sequences.
Value
A character string vector of the alignment, with dots in the
conserved positions.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
See Also
Examples
1
2
3
4
5
6
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
strs <- DottedAlignment(lst$hseqs)
# Create a data frame to visualize the result.
data.frame(Hpl=strs,stringsAsFactors=FALSE)
QSutils documentation built on Nov. 8, 2020, 7:42 p.m.
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Description Usage Arguments Value Author(s) See Also Examples
View source: R/DottedAlignment.R
Description
Given an alignment, it takes the first sequence as reference, and depicts all equivalences in the alignment as dots, leaving only the variants with respect to the reference.
Usage
1 | DottedAlignment(hseqs)
|
Arguments
hseqs |
DNAStringSet or AAStringSet with haplotype sequences. |
Value
A character string vector of the alignment, with dots in the conserved positions.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
See Also
Examples
1 2 3 4 5 6 | filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
strs <- DottedAlignment(lst$hseqs)
# Create a data frame to visualize the result.
data.frame(Hpl=strs,stringsAsFactors=FALSE)
|
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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