ReportVariants: Report variants
In QSutils: Quasispecies Diversity

Description Usage Arguments Value Author(s) References Examples

Reports the variants of a DNAStringSet or AAStringSet of haplotypes given a reference sequence.

1	ReportVariants(hseqs,ref.seq,nr=NULL,start=1)

`hseqs`	DNAStringSet or AAstringSet object of the aligned haplotypes.
`ref.seq`	Character vector with the reference sequence of the alignment.
`nr`	Numeric vector with the abundances of each haplotype in hseqs. When `nr` is NULL, a vector of ones is taken as default.
`start`	Position of the first nucleotide in the alignment

A dataframe with 4 columns: the nucleotide in the reference sequence, the position, the variant nucleotide, and its abundance.

Mercedes Guerrero-Murillo and Josep Gregori

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.

# Load objects.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")

# Report the variants in these haplotypes,
# taking as a reference the most abundant haplotype.
ReportVariants(lst$hseqs[-1], ref.seq= as.character(lst$hseqs[1]), 
lst$nr[-1], start = 1)