SummaryMuts: Distribution of nucleotides or amino acids in polymorphic...

In VHIRHepatiques/QSutils: Quasispecies Diversity

Distribution of nucleotides or amino acids in polymorphic sites

Description

Computes the nucleotide or amino acid frequencies at all polymorphic sites in the alignment.

Usage

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

ReadAmplSeqs

Examples

# 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)

VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.