R/dataset-li2017.R

In isotracer: Isotopic Tracer Analysis Using MCMC

#' Protein degradation in Arabidopsis plants (Li et al. 2017)
#'
#' Dataset built from the Dryad depository entry associated with the article
#' "Protein degradation rate in Arabidopsis thaliana leaf growth and development"
#' by Li et al. (2017)
#'
#' In this study, the authors used a growth medium containing 15N to grow
#' 21-day old Arabidopsis plants which were grown on a natural 14N/15N medium
#' until that day. The third, fifth and seventh leaves were sampled from
#' individuals at different time points after the medium switch (0, 1, 3 and 5
#' days). Proteins were identified and labelled fractions were measured using
#' mass spectrometry. Relative protein abundances were determined in comparison
#' with a reference sample.
#'
#' The aim of the authors was to quantify in vivo degradation rates for as many
#' proteins as possible (1228 proteins in the original paper) and examine which
#' determinants had an effect or not on protein degradation rates (e.g. protein
#' domains, protein complex membership, ...).
#'
#' Three datasets were extracted from the large dataset available on Dryad for
#' packaging inside isotracer: \code{li2017}, \code{li2017_prots}, and
#' \code{li2017_counts}.
#'
#' @format \code{li2017} is the main dataset and is a tibble with columns:
#' \describe{
#'   \item{prot_id}{Protein identifier. Can be matched to a more explicit
#'     protein description in \code{li2017_prots}.}
#'   \item{sample}{Sample identity. Different samples were used for relative
#'     abundance measurements and labelled fraction measurements.}
#'   \item{rel_abundance}{Relative abundance compared to a reference sample.}
#'   \item{labeled_fraction}{Proportion of 15N in the protein.}
#'   \item{time_day}{Time elapsed since growth medium switch to 15N, in days.}
#'   \item{leaf_id}{Leaf identity (3rd, 5th, or 7th leaf of individual plants).}
#' }
#'
#' @format \code{li2017_prots} maps protein identifiers to protein descriptions
#'     and is a tibble with columns:
#' \describe{
#'   \item{prot_id}{Protein identifier. Can be matched with the same column in
#'     \code{li2017}.}
#'   \item{description}{Protein description}
#' }
#'
#' @format \code{li2017_counts} is a summary table counting the number of
#'     available data points for relative abundance and labelled fraction for
#'     each protein in \code{li2017}. It is a tibble with columns:
#' \describe{
#'   \item{prot_id}{Protein identifier. Can be matched with the same column in
#'     \code{li2017}.}
#'   \item{n_abundance_data}{Number of relative abundance data points for a
#'     given protein.}
#'   \item{n_labelling_data}{Number of labelled fraction data points for a
#'     given protein.}
#' }
#' 
#' @source Data was taken from the following Dryad repository: Li, Lei, Clark
#'     J. Nelson, Josua Troesch, Ian Castleden, Shaobai Huang, and A. Harvey
#'     Millar. “Data from: Protein Degradation Rate in Arabidopsis Thaliana
#'     Leaf Growth and Development.” Dryad,
#'     2018. https://doi.org/10.5061/DRYAD.Q3H85.
#'
#' @source The Dryad repository was associated with the following paper: Li,
#'     Lei, Clark J. Nelson, Josua Trösch, Ian Castleden, Shaobai Huang, and
#'     A. Harvey Millar. “Protein Degradation Rate in Arabidopsis Thaliana Leaf
#'     Growth and Development.” The Plant Cell 29, no. 2 (February 1, 2017):
#'     207–28. https://doi.org/10.1105/tpc.16.00768.
#'
#' @aliases li2017_prots li2017_counts

"li2017"