ConsSeq: Consensus sequence given an alignment and frequencies
In VHIRHepatiques/QSutils: Quasispecies Diversity
ConsSeq R Documentation
Consensus sequence given an alignment and frequencies
Description
ConsSeq determines the consensus sequence from a set of haplotypes.
Usage
ConsSeq(seqs, w=NULL)
Arguments
seqs
DNAStringSet or AAStringSet object with the haplotype sequences.
w
An optional numeric vector with the haplotype counts.
Details
The most frequent nucleotide or amino acid at each position is taken. No
IUPAC ambiguity codes are considered; in the case of ties, the consensus
nucleotide is decided randomly.
Value
Character vector with the consensus sequence.
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")
ConsSeq(lst$hseqs,lst$nr)
VHIRHepatiques/QSutils documentation built on April 12, 2024, 12:25 p.m.
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| ConsSeq | R Documentation |
Consensus sequence given an alignment and frequencies
Description
ConsSeq determines the consensus sequence from a set of haplotypes.
Usage
ConsSeq(seqs, w=NULL)
Arguments
seqs |
DNAStringSet or AAStringSet object with the haplotype sequences. |
w |
An optional numeric vector with the haplotype counts. |
Details
The most frequent nucleotide or amino acid at each position is taken. No IUPAC ambiguity codes are considered; in the case of ties, the consensus nucleotide is decided randomly.
Value
Character vector with the consensus sequence.
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")
ConsSeq(lst$hseqs,lst$nr)
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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