# Code for documenting the datasets
#' Sample Data
#'
#' A dataset containing subsample from a single tenplex
#'
#' @format A single dataframe containing the
#' same 14 columns. The first three rows of each dataframe constitute a data
#' header that will be used to specify the correct model to use in the data
#' analysis. The 14 columns must all be present and must have the names seen in
#' this example.
#' \describe{
#' \item{Protein}{A string that identifies the protein or protein group for
#' which relative estimates will be computed. The first three rows of this
#' column must have 0 or 1 entries with a 1 denoting the use of the relevant
#' header row. The first row is used to specify conditions for the signal to
#' noise columns. Since conditions must always be present, it does not matter
#' if a 0 or 1 is used here. The indicator in the second row lets us know if
#' biological replicates are to be defined in the second row (they might
#' alternatively be defined in column 3). The third and final header row is
#' used to identify post-translational modifications. If these are used a 1 must
#' be entered into row 3 column 1. }
#' \item{Peptide}{Unique peptide identifier. Only used in PTM analyses but the
#' column must be present. Header entries here are irrelevant.}
#' \item{bioID}{This column may be used to denote biological replicates. Either
#' strings or numbers can be used, to key point being that any entries with the
#' same value will be treated as biological replicates. Depending on the data
#' source, specifying this in a column header may not be practical, which is why
#' the option to specify biological replicates within each row has been made
#' available. Entries to the header rows in this column are irrelevant with the
#' exception of Row 1 which indicates whether or not the column is being used.}
#' \item{Covariate}{This column provides a continuous covariate to be used in a
#' compositional non-linear regression. Typically these entries will either be
#' summed signal-to-noise values or isolation specificities. If a covariate is
#' to be used, a one must be entered in the first row of this column. The
#' second and third rows do nothing.}
#' \item{varCat}{This column provides a way to allow for additional variance
#' components. Separate variance components are always generated for each
#' plex/tag combination. However, it might be of interest to further
#' separate variance accoriding to some other factor that varies within a
#' tag, e.g. species. This is accomplished by adding a categorical variable
#' for variance groups. Observations beloning to the same category should
#' have the same category entry (either an integer or string). These
#' categories are only intended for protein analysis and have no bearing on
#' PTM's (beyond altering the protein results). A 1 must be entered into the
#' first row of theheader when using this column.}
#' \item{tag1-tagN}{These columns contain signal to noise intensity ratios.
#' The column names are case sensitive and must include the string 'tag'
#' followed by a number. The entries in the first three rows of these columns
#' are used to tell the program which columns represent various conditions,
#' biological replicates, and PTMs (not currently in use). Columns with the
#' same entry in row 1 are considered to be from the same condition (this
#' determines what comparisons will be made). Similarly equivalent values in
#' row two will determine which columns are biological replicates. The same
#' value in the third column denotes the same type of PTM, e.g. 1 =
#' phosphorylation and 2 = ubiqutination. Ten columns are not necessary as the program accepts
#' an arbitrary number of tag columns. Values are assumed to represent signal
#' to noise measurements. Accordingly any values that are missing or less than
#' one will be replaced with 1's during data processing.}
#' }
#'
#'
"sampleDat"
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