IntersectStrandHpls: Forward and reverse strand haplotype intersections

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/IntersectStrandHpls.R

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

1
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

1
2
3
4
5
6
7
8
# 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)

VHIRHepatiques/QSutils documentation built on Oct. 24, 2018, 12:06 p.m.