R/data-se_soybean_ir_sub.R

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#' Raw and subsetted soybean leaves data SummarizedExperiment object
#'
#' @name se_soybean_ir_sub
#' @title Raw and subsetted soybean leaves iron-metabolism SummarizedExperiment
#' @description This dataset contains raw RNA-sequencing read counts from a 
#' soybean dataset that compared leaves that were exposed to iron-rich (iron
#' -postive) soil conditions versus leaves that were exposed to iron-poor 
#' (iron-negative) soil conditions. The data was collected 120 minutes after 
#' iron conditions were initiated. To save on size, this example dataset was 
#' generated by obtaining a random subset of 1 out of 10 genes from the 
#' original resource.
#' @docType data
#' @format (1) A DelayedMatrix with 5,604 rows and 7 variables and 1 row per
#' gene. Accessible by \code{assay(se_soybean_ir_sub)}. (2) A List with 1
#' list element per treatment group combination and 1 row per gene.
#' Accessible by \code{rowData(se_soybean_ir_sub)}.
#' @details
#' \itemize{
    #' \item \code{assay(se_soybean_ir_sub)} Structure:
    #' \item N.1 iron-negative condition replicate 1 raw read counts
    #' \item N.2 iron-negative condition replicate 2 raw read counts
    #' \item N.3 iron-negative condition replicate 3 raw read counts
    #' \item P.1 iron-positive condition replicate 1 raw read counts
    #' \item P.2 iron-positive condition replicate 2 raw read counts
    #' \item P.3 iron-positive condition replicate 3 raw read counts
    #' }
    #' 
#' \itemize{
#' \item \code{rowData(se_soybean_ir_sub)} list element Structure:
#' \item ID gene name
#' \item logFC log fold change
#' \item logCPM log counts per million
#' \item LR likelihood ratio
#' \item PValue p-value
#' \item FDR FDR value
#' }
#' @keywords datasets
#' @usage data(se_soybean_ir_sub)
#' @format A data frame with 5,604 rows and 7 variables
#' @seealso \code{\link{soybean_ir_sub}} and
#' \code{\link{soybean_ir_sub_metrics}}
#' @references
#' Moran Lauter AN, Graham MA. NCBI SRA bioproject accession: PRJNA318409.
#' 
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