DBrule {QSutils} | R Documentation |
Computes the nearest cluster to a given sequence.
DBrule(grpDist, hr, oDist, g.names = NULL)
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. |
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. |
Mercedes Guerrero-Murillo and Josep Gregori
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.
# 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