DBrule {QSutils} | R Documentation

## Genotyping by the DB rule

### Description

Computes the nearest cluster to a given sequence.

### Usage

    DBrule(grpDist, hr, oDist, g.names = NULL)

### Arguments

`grpDist` | Distances between reference sequences.
`hr` | Factor or a vector of integers that contains the type or subtype for each reference sequence.
`oDist` | Distance from the sequence to be classified to the reference sequences.
`g.names` | Type or subtype names to classify the sequence.

### Value

List with three elements:

`Phi2` | Vector with the distances to each cluster.
`DB.rule` | The index of the nearest cluster.
`Type` | Name of the nearest cluster.

### Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

### References

Caballero A, Gregori J, Homs M, Tabernero D, Gonzalez C, Quer J, Blasi M, Casillas R, Nieto L, Riveiro-Barciela M, Esteban R, Buti M, Rodriguez-Frias F. Complex Genotype Mixtures Analyzed by Deep Sequencing in Two Different Regions of Hepatitis B Virus. PLoS One. 2015 Dec 29;10(12):e0144816. doi: 10.1371/journal.pone.0144816. eCollection 2015. PubMed PMID: 26714168; PubMed Central PMCID: PMC4695080.

### Examples

    # Load haplotype to be genotyped.
    filepath<-system.file("extdata","Unknown-Genotype.fna", package="QSutils")
    lst <- ReadAmplSeqs(filepath,type="DNA")
    hseq <- lst$hseq[1]

    # Load genotype references.
    filepath_geno<-system.file("extdata","GenotypeStandards_A-H.fas",
    package="QSutils")
    RefSeqs <- readDNAStringSet(filepath_geno)

    # Compute pairwise distances.
    dm <- as.matrix(DNA.dist(c(hseq,RefSeqs),model="K80"))

    # Distances between genotype RefSeqs
    dgrp <- dm[-1,-1]
    grp <- factor(substr(rownames(dgrp),1,1))
    hr <- as.integer(grp)

    # Distance of the query haplotype to the reference sequence.
    d <- dm[1,-1]

    # Genotyping by the DB rule.
    dsc <- DBrule(dgrp,hr,d,levels(grp))
    dsc

[Package QSutils version 1.12.0 Index]