#' Assign Taxonomy
#' Uses DADA2's assignTaxonomy function to assign taxa to ASV sequences.
#'
#' @param seqtab Sequence frequency table
#' @param object S4 object of type fastq2otu (i.e. fastPaired, fastSingle)
#' @importFrom dada2 assignTaxonomy
#' @return OTU table
#'
assignSeqTaxonomy <- function(seqtab, object) {
# Load required libraries
# Extract required parameters
referenceDatabase <- object@taxDatabase
minBootstrap <- object@assignTaxMinBootstrap
tryComplement <- object@assignTaxTryComplement
showBootstraps <- object@assignTaxOutputBootstraps
taxLevels <- object@assignTaxLevels
multithread <- object@assignTaxMultiThread
verbose <- object@assignTaxVerbose
# Execute assignTaxonomy()
otu.tab <- dada2::assignTaxonomy(as.matrix(seqtab), referenceDatabase, minBoot = minBootstrap,
tryRC = tryComplement, outputBootstraps = showBootstraps,
taxLevels = taxLevels, multithread = multithread,
verbose = verbose)
# Return OTU table
return(otu.tab)
}
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