SummaryMuts {QSutils} | R Documentation

## 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)

[Package QSutils version 1.12.0 Index]