IntersectStrandHpls {QSutils} | R Documentation

## Forward and reverse strand haplotype intersections

### 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)

[Package QSutils version 1.4.0 Index]