% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/opsDesign.R
 \name{getBarcodeDistanceMatrix}
 \alias{getBarcodeDistanceMatrix}
 \title{Get distance between query and target sets of barcodes}
 \usage{
 getBarcodeDistanceMatrix(
   queryBarcodes,
   targetBarcodes = NULL,
   binnarize = TRUE,
   min_dist_edit = NULL,

   dist_method = c("hamming", "levenshtein"),

   ignore_diagonal = TRUE,
   splitByChunks = FALSE,
   n_chunks = NULL
 )
 }
 \arguments{

 \item{queryBarcodes}{Character vector of DNA sequences or DNAStringSet.}

 \item{targetBarcodes}{Optional character vector of DNA sequences 
 or DNAStringSet. If NULL, distances will be calculated between
 barcodes provided in \code{queryBarcodes}.}

 
 \item{binnarize}{Should the distance matrix be made binnary?
 TRUE by default. See details section.}
 
 \item{min_dist_edit}{Integer specifying the minimum distance edit

 required for barcodes to be considered dissimilar when
 \code{binnarize=TRUE}, ignored otherwise.}

 
 \item{dist_method}{String specifying distance method. Must be

 either "hamming" (default) or "levenshtein".}

 
 \item{ignore_diagonal}{When \code{targetBarcodes=NULL}, should the
 diagonal distances be set to 0 to ignore self distances?
 TRUE by default.}
 
 \item{splitByChunks}{Should distances be calculated in a chunk-wise

 manner? FALSE by default. Highly recommended when the set of query

 barcodes is large to reduce memory footprint.}
 
 \item{n_chunks}{Integer specifying the number of chunks to be used
 when \code{splitByChunks=TRUE}. If NULL (default), number of chunks
 will be chosen automatically.}
 }
 \value{
 A sparse matrix of class \code{dgCMatrix} or \code{dsCMatrix}
     in which rows correspond to \code{queryBarcodes} and columns
     correspond to \code{targetBarcodes}. If \code{binnarize=TRUE},
     a value of 0 indicates that two barcodes have a distance 
     greater of equal to \code{min_dist_edit}, otherwise the value 
     is 1. If If \code{binnarize=FALSE}, values represent
     the actual calculated distances between barcodes.
 }
 \description{
 Get distance between query and target sets of barcodes
 }
 \examples{

 data(guideSetExample, package="crisprDesign")

 guideSetExample <- addOpsBarcodes(guideSetExample)
 barcodes <- as.character(guideSetExample$opsBarcode)

 dist <- getBarcodeDistanceMatrix(barcodes, min_dist_edit=2)

 
 }
 \author{
 Jean-Philippe Fortin
 }