ReportVariants: Report variants

Description Usage Arguments Value Author(s) References Examples

Description

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

Usage

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

Arguments

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

Value

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

Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

References

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.

Examples

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# 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)

VHIRHepatiques/QSutils documentation built on May 8, 2019, 1:44 p.m.