R/vignette_data.R

In epivizrChart: R interface to epiviz web components

#' Example methylation data (blocks) for epivizr vignette.
#'
#' Example results from methylation analysis of human chromosome 11 using the `minfi` package
#' of TCGA 450k beadarray samples. This object contains large regions of methylation difference between tumor
#' and normal samples obtained from [`minfi::blockFinder()`].
#'
#' @format A `GenomicRanges::GRanges` object with 129 and \code{mcols}:
#'
#' \describe{
#'  \item{\code{value}}{average smooth methylation difference within block}
#'  \item{\code{area}}{block area estimate (abs(value) * length)}
#'  \item{\code{cluster}}{id of cluster blockgroup within which block occurs}
#'  \item{\code{indexStart}}{index of first cluster in block}
#'  \item{\code{indexEnd}}{index of last cluster in block}
#'  \item{\code{L}}{number of clusters in block}
#'  \item{\code{clusterL}}{number of probes in block}
#'  \item{\code{p.value}}{permutation p.value based on difference conditioned on length}
#'  \item{\code{fwer}}{family-wise error rate estimate based on difference conditioned on length}
#'  \item{\code{p.valueArea}}{permutation p.value based on area}
#'  \item{\code{fwerArea}}{family-wise error rate estimate based on area}
#' }
#' @source TCGA project: \url{https://tcga-data.nci.nih.gov/tcga/}
#' @name tcga_colon_blocks
#' @usage data(tcga_colon_blocks)
#' @docType data
#' @md
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#' Example methylation data (smoothed methylation levels) for epivizr vignette
#'
#' Example results from methylation analysis of human chromosome 11 using the `minfi` package
#' of TCGA 450k beadarray samples. This object contains probe cluster level methylation estimates from
#' [`minfi::blockFinder()`].
#'
#' @format A `GenomicRanges::GRanges` object with 7135 ranges and \code{mcols}:
#'
#' \describe{
#'  \item{\code{id}}{probe cluster id}
#'  \item{\code{type}}{probe cluster type}
#'  \item{\code{blockgroup}}{probe cluster block group}
#'  \item{\code{diff}}{raw methylation percentage difference between normal and tumor}
#'  \item{\code{smooth}}{smooth methylation percentage difference between normal and tumor}
#'  \item{\code{normalMean}}{mean methylation estimate for normal samples}
#'  \item{\code{cancerMean}}{mean methylation estimate for cancer samples}
#' }
#'
#' @source TCGA project: \url{https://tcga-data.nci.nih.gov/tcga/}
#' @name tcga_colon_curves
#' @usage data(tcga_colon_curves)
#' @docType data
#' @md
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#' Example exon-level RNAseq data from TCGA project for epivizr vignette.
#'
#' A `SummarizedExperiment::RangedSummarizedExperiment` object containing exon-level
#' counts from RNAseq data for colon tumor and normal tissue from the TCGA project.
#' Only exons in human chromosome 11 are included.
#'
#' @format A `SummarizedExperiment::RangedSummarizedExperiment` object with 12,800 rows (exons) and 40 samples.
#'  \describe{
#'    \item{\code{assay(tcga_colon_expression)}}{exon-level count matrix}
#'    \item{\code{colData(tcga_colon_expression)}}{a \code{DataFrame} containing sample information.
#'      Normal/Tumor status is given in column \code{sample_type}}
#'  }
#'
#' @source TCGA project: \url{https://tcga-data.nci.nih.gov/tcga/}
#' @name tcga_colon_expression
#' @usage data(tcga_colon_expression)
#' @docType data
#' @md
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#' Example SummarizedExperiment for epivizr vignette
#' @format A `SummarizedExperiment::RangedSummarizedExperiment` object.
#' @docType data
#' @usage data(sumexp)
#' @name sumexp
#' @md
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#' Example expression data from the Gene Expression barcode project
#'
#' See vignette `data_preprocessing` for code to build this object.
#'
#' @format An `Biobase::ExpressionSet` object
#' @docType data
#' @usage data(bcode_eset)
#' @name bcode_eset
#' @md
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#' Locations of CpG Islands
#'
#' @format A `GenomicRanges::GRanges` object with locations of CpG Islands in hg19
#' @docType data
#' @usage data(cgi_gr)
#' @name cgi_gr
#' @md
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