DBrule: Genotyping by the DB rule

In QSutils: Quasispecies Diversity

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

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