DBrule: Genotyping by the DB rule

Description Usage Arguments Value Author(s) References Examples

View source: R/DBrule.R

Description

Computes the nearest cluster to a given sequence.

Usage

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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

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# 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

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