SortByMutations {QSutils} | R Documentation

## Sort haplotypes by mutations and abundance

### Description

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

### Usage

    SortByMutations(bseqs, nr)

### Arguments

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

### Details

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.

### Value

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.

### Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

### References

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.

### 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")

    SortByMutations(lst$hseq,lst$nr)

[Package QSutils version 1.12.0 Index]