R/grin.results.R

In GRIN2: Genomic Random Interval (GRIN)

#' Example GRIN2 Analysis Results
#'
#' A precomputed GRIN2 results object generated from the example genomic lesion
#' dataset included with the package. The object represents a standard
#' gene-level GRIN2 analysis and is provided for use in examples of downstream
#' analysis, visualization, and export functions without repeatedly running
#' [grin.stats()].
#'
#' The object was generated using:
#'
#' \preformatted{
#' grin.results <- grin.stats(
#'   lsn.data = lesion_data,
#'   gene.data = hg38_gene_annotation,
#'   chr.size = hg38_chrom_size
#' )
#' }
#'
#' @format A named list containing the following 10 components:
#'
#' \describe{
#'
#'   \item{\code{gene.hits}}{
#'   A data frame containing the primary GRIN2 analysis results for each gene,
#'   including lesion counts, affected-subject counts, lesion-specific
#'   probabilities, p-values, q-values, and constellation test statistics.
#'   }
#'
#'   \item{\code{lsn.data}}{
#'   The genomic lesion dataset used as input to \code{\link{grin.stats}}.
#'   Each row corresponds to a genomic lesion together with its genomic
#'   coordinates, lesion type, and subject identifier.
#'   }
#'
#'   \item{\code{gene.data}}{
#'   The gene annotation data used during the analysis, including genomic
#'   coordinates and gene identifiers.
#'   }
#'
#'   \item{\code{gene.lsn.data}}{
#'   A data frame describing overlaps between genomic lesions and genes.
#'   }
#'
#'   \item{\code{chr.size}}{
#'   Chromosome target sizes used for probability calculations.
#'   }
#'
#'   \item{\code{gene.index}}{
#'   Internal index used to efficiently identify chromosome-specific groups of
#'   genes during the analysis.
#'   }
#'
#'   \item{\code{lsn.index}}{
#'   Internal index used to efficiently identify chromosome-specific groups of
#'   genomic lesions during the analysis.
#'   }
#'
#'   \item{\code{gene.exon.size}}{
#'   Gene-specific exon target sizes used for exon-level analyses.
#'   This component is \code{NULL} for the standard gene-level example.
#'   }
#'
#'   \item{\code{exon.chrom.size}}{
#'   Chromosome exon target sizes used for exon-level analyses.
#'   This component is \code{NULL} for the standard gene-level example.
#'   }
#'
#'   \item{\code{exon_level}}{
#'   Indicates which lesion types were modeled using exon-level target sizes.
#'   This component is \code{NULL} for the standard gene-level example.
#'   }
#' }
#'
#' @details
#' This dataset is intended primarily for package examples and demonstrations.
#' It allows downstream GRIN2 functions to be illustrated without repeatedly
#' running \code{\link{grin.stats}}. The object contains the complete output
#' returned by \code{\link{grin.stats}} and can therefore be supplied directly
#' to functions that require a GRIN2 results object.
#'
#' @source Generated from the example datasets
#' \code{lesion_data}, \code{hg38_gene_annotation}, and
#' \code{hg38_chrom_size} included with the GRIN2 package.
#'
#' @seealso
#' \code{\link{grin.stats}},
#' \code{\link{lsn.transcripts.plot}},
#' \code{\link{grin.oncoprint.mtx}},
#' \code{\link{write.grin.xlsx}}
#'
#' @examples
#' data("grin.results")
#'
#' # Display the available components.
#' names(grin.results)
#'
#' # View the first few rows of the primary results table.
#' head(grin.results$gene.hits)
#'
#' @name grin.results
#' @docType data
#' @keywords datasets
NULL