R/tzara-package.R

In brendanf/tzara: Cluster long amplicons using dada2 denoising on variable regions

#' @keywords internal
"_PACKAGE"

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# roxygen namespace tags. Modify with care!
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NULL

#' Sample amplicon sequences
#'
#' These are the three most abundant ASVs from
#' \href{https://www.authorea.com/doi/full/10.22541/au.160340221.18389016/v1}{Furneaux et al. 2020}.
#' They are derived from PacBio RSII metabarcoding of soil samples from
#' central Benin, West Africa.
#' The three sequences are from the fungal genera \emph{Penicillium}, \emph{Agaricus}
#' (included as a control), and \emph{Inocybe}.
#'
#' @format A \code{\link[Biostrings]{DNAStringSet}} with three sequences.
"tzara_sample"

#' Sample quality scores
#'
#' These are based on CCS quality scores from 1000 randomly sampled reads of
#' long amplicon PacBio RSII samples in
#' \href{https://www.authorea.com/doi/full/10.22541/au.160340221.18389016/v1}{Furneaux et al. 2020}.
#' All the reads were at least 1000 bp.
#'
#' @format An \code{integer matrix} where rows represent a single sequence,
#' columns are named by fastq quality score characters, and values are the
#' number of times each character appears in each sequence.
"quality_profile"