IntersectStrandHpls: Forward and reverse strand haplotype intersections

In QSutils: Quasispecies Diversity

Description

Computes the intersection of forward and reverse strand haplotypes after a previous abundance filter that removes strand haplotypes below a given frequency threshold or unique to a single strand.

Usage

IntersectStrandHpls(nrFW, hseqsFW, nrRV, hseqsRV, thr = 0.001)

Arguments

nrFW	Numeric vector with forward strand haplotype counts.
hseqsFW	DNAStringSet object with the forward strand haplotypes.
nrRV	Numeric vector with forward reverse strand haplotypes.
hseqsRV	DNAStringSet object with the reverse strand haplotypes.
thr	Threshold to filter haplotypes at minimum abundance.

Value

List object with this elements:

hseqs	DNAStringSet object with the forward and reverse strand intersected.
nr	Numeric vector with the abundance of each haplotype.
pFW	Vector of abundances of aligned forward strand.
pRV	Vector of abundances of aligned reverse strand.

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.

See Also

ReadAmplSeqs

Examples

# Load objects.
filepath_FW<-system.file("extdata","ToyData_FWReads.fna", package="QSutils")
FW<- ReadAmplSeqs(filepath_FW,type="DNA")
filepath_RV<-system.file("extdata","ToyData_RVReads.fna", package="QSutils")
RV<- ReadAmplSeqs(filepath_RV,type="DNA")

# Intersect the two objects, with a default threshold.
IntersectStrandHpls(FW$nr,FW$hseqs,RV$nr,RV$hseqs)

QSutils documentation built on Nov. 8, 2020, 7:42 p.m.