SortByMutations: Sort haplotypes by mutations and abundance
In QSutils: Quasispecies Diversity

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

Sorts and renames haplotypes by the number of mutations with respect to the dominant haplotype, and by abundance.

1	SortByMutations(bseqs, nr)

`bseqs`	DNAStringSet or AAStringSet object with the haplotype alignment.
`nr`	Vector with the haplotype counts.

The haplotypes are pairwise-aligned to the dominant haplotype and then sorted: first, by decreasing order of the number of differences with respect to the dominant haplotype, and second, by decreasing order of abundance. As a result, haplotypes are renamed according to the pattern Hpl.n.xxxx, where n represents the number of differences, and xxxx the abundance order within the mutation number.

Returns a list with three elements.

`bseqs`	DNAStringSet or AAStringSet with the haplotype sequences.
`nr`	Vector of the haplotype counts.
`nm`	Vector of the number of differences of each haplotype with respect to the dominant haplotype.

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

SortByMutations(lst$hseq,lst$nr)