SortByMutations: Sort haplotypes by mutations and abundance

In VHIRHepatiques/QSutils: Quasispecies Diversity

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)

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