SummaryMuts: Distribution of nucleotides or amino acids in polymorphic...
In QSutils: Quasispecies Diversity
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
Description
Computes the nucleotide or amino acid frequencies at all polymorphic sites
in the alignment.
Usage
1
SummaryMuts(seqs, w = NULL, off = 0)
Arguments
seqs
DNAStringSet or AAStringSet with the haplotype sequences.
w
An optional numeric vector with the haplotype counts. When w is NULL,
a vector of ones is taken as default.
off
Offset of first position in the alignment.
Value
Data frame with the polymorphic positions and nucleotide or amino
acid frequencies.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
References
Gregori J, Esteban JI, Cubero M, Garcia-Cehic D, Perales C, Casillas R,
Alvarez-Tejado M, Rodríguez-Frías F, Guardia J, Domingo E, Quer J. Ultra-deep
pyrosequencing (UDPS) data treatment to study amplicon HCV minor variants. PLoS
One. 2013 Dec 31;8(12):e83361. doi: 10.1371/journal.pone.0083361. eCollection
2013. PubMed PMID: 24391758; PubMed Central PMCID: PMC3877031.
Ramírez C, Gregori J, Buti M, Tabernero D, Camós S, Casillas R, Quer J,
Esteban R, Homs M, Rodriguez-Frías F. A comparative study of ultra-deep
pyrosequencing and cloning to quantitatively analyze the viral quasispecies
using hepatitis B virus infection as a model. Antiviral Res. 2013
May;98(2):273-83. doi: 10.1016/j.antiviral.2013.03.007. Epub 2013
Mar 20. PubMed PMID: 23523552.
See Also
Examples
1
2
3
4
5
6
# Load haplotype alignment with abundances.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
# Distribution of nucleotides at polymorphic sites.
SummaryMuts(lst$hseqs,lst$nr,off=0)
QSutils documentation built on Nov. 8, 2020, 7:42 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
Description
Computes the nucleotide or amino acid frequencies at all polymorphic sites in the alignment.
Usage
1 | SummaryMuts(seqs, w = NULL, off = 0)
|
Arguments
seqs |
DNAStringSet or AAStringSet with the haplotype sequences. |
w |
An optional numeric vector with the haplotype counts. When |
off |
Offset of first position in the alignment. |
Value
Data frame with the polymorphic positions and nucleotide or amino acid frequencies.
Author(s)
Mercedes Guerrero-Murillo and Josep Gregori
References
Gregori J, Esteban JI, Cubero M, Garcia-Cehic D, Perales C, Casillas R, Alvarez-Tejado M, Rodríguez-Frías F, Guardia J, Domingo E, Quer J. Ultra-deep pyrosequencing (UDPS) data treatment to study amplicon HCV minor variants. PLoS One. 2013 Dec 31;8(12):e83361. doi: 10.1371/journal.pone.0083361. eCollection 2013. PubMed PMID: 24391758; PubMed Central PMCID: PMC3877031.
Ramírez C, Gregori J, Buti M, Tabernero D, Camós S, Casillas R, Quer J, Esteban R, Homs M, Rodriguez-Frías F. A comparative study of ultra-deep pyrosequencing and cloning to quantitatively analyze the viral quasispecies using hepatitis B virus infection as a model. Antiviral Res. 2013 May;98(2):273-83. doi: 10.1016/j.antiviral.2013.03.007. Epub 2013 Mar 20. PubMed PMID: 23523552.
See Also
Examples
1 2 3 4 5 6 | # Load haplotype alignment with abundances.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
# Distribution of nucleotides at polymorphic sites.
SummaryMuts(lst$hseqs,lst$nr,off=0)
|
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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