DottedAlignment: Align haplotypes into a dotted alignment
In VHIRHepatiques/QSutils: Quasispecies Diversity
View source: R/DottedAlignment.R
DottedAlignment R Documentation
Align haplotypes into a dotted alignment
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
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
ReadAmplSeqs
Examples
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
strs <- DottedAlignment(lst$hseqs)
# Create a data frame to visualize the result.
data.frame(Hpl=strs,stringsAsFactors=FALSE)
VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.
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View source: R/DottedAlignment.R
| DottedAlignment | R Documentation |
Align haplotypes into a dotted alignment
Description
Given an alignment, it takes the first sequence as reference, and depicts all equivalences in the alignment as dots, leaving only the variants with respect to the reference.
Usage
DottedAlignment(hseqs)
Arguments
hseqs |
DNAStringSet or AAStringSet with haplotype sequences. |
Value
A character string vector of the alignment, with dots in the conserved positions.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
See Also
ReadAmplSeqs
Examples
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
strs <- DottedAlignment(lst$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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