ConsSeq: Consensus sequence given an alignment and frequencies
In QSutils: Quasispecies Diversity
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
ConsSeq determines the consensus sequence from a set of haplotypes.
Usage
1
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
Examples
1
2
3
4
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
ConsSeq(lst$hseqs,lst$nr)
QSutils documentation built on Nov. 8, 2020, 7:42 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
ConsSeq determines the consensus sequence from a set of haplotypes.
Usage
1 |
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
Examples
1 2 3 4 | 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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