MutsTbl: Table of mutation frequencies by position
In QSutils: Quasispecies Diversity

Description Usage Arguments Value Author(s) References See Also Examples

Computes the table of mutation frequencies by position with respect to the alignment consensus.

1	MutsTbl(hseqs,nr=NULL)

`hseqs`	DNAStringSet or AAStringSet with the aligned haplotype sequences.
`nr`	An optional numeric vector with the haplotype counts. When `nr` is NULL, the same weight is given to each haplotype.

Matrix of mutation counts by position. A (4 x n) or (20 x n) matrix, where n is the alignment length.

Mercedes Guerrero-Murillo and Josep Gregori

Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.

Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.

ReadAmplSeqs

# Load the haplotypes alignment with abundances.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")

# Table of mutations in the alignment, regardless of haplotype abundance. 
MutsTbl(lst$hseqs)

# Table of mutations taking into account abundance.
MutsTbl(lst$hseqs,lst$nr)