R/data.R

In ordinalbayes: Bayesian Ordinal Regression for High-Dimensional Data

#' Subset of The Cancer Genome Atlas Cervical Cancer HTSeq Data.
#'
#' This subset includes 2,009 transcripts and four phenotypic variables for
#' 242 subjects with squamous cell cervical cancer.
#'
#' @format The format is of formal class 'DESeqTransform' (package "DESeq2") with the following extractor functions:
#' \describe{
#'   \item{assay}{includes rld transformed transcript expression data}
#'   \item{colData}{includes phenotypic data: \code{age_at_index}, \code{cigarettes_per_day}, \code{race}, and \code{Stage}}
#' }
#' @source TCGAbiolinks TCGA-CESC
#' @import DESeq2
#' @import SummarizedExperiment
#' @keywords datasets
"finalSet"

#' Smaller Subset of The Cancer Genome Atlas Cervical Cancer HTSeq Data.
#'
#' This subset includes 41 transcripts and four phenotypic variables for
#' 242 subjects with squamous cell cervical cancer.
#'
#' @format The format is of formal class 'DESeqTransform' (package "DESeq2") with the following extractor functions:
#' \describe{
#'   \item{assay}{includes rld transformed transcript expression data}
#'   \item{colData}{includes phenotypic data: \code{age_at_index}, \code{cigarettes_per_day}, \code{race}, and \code{Stage}}
#' }
#' @source TCGAbiolinks TCGA-CESC
#' @import DESeq2
#' @import SummarizedExperiment
#' @keywords datasets
"reducedSet"

#' Data Frame of Smaller Subset of The Cancer Genome Atlas Cervical Cancer HTSeq Data.
#'
#' This data.frame is a subset that includes 41 transcripts and four phenotypic variables for
#' 242 subjects with squamous cell cervical cancer.
#'
#' @format This \code{data.frame} includes the following variables:
#' \describe{
#'   \item{age_at_index}{a numeric vector storing age at cervical cancer diagnosis.}
#'   \item{cigarettes_per_day}{a numeric vector storing the number of cigarettes smoked per day.}
#'   \item{race}{a character vector representing race of the subject.}
#'   \item{Stage}{an ordered factor representing stage of cervical cancer.}
#'   \item{ENSG00000076344}{a numeric vector representing expression of ENSG00000076344.}
#'   \item{ENSG00000077274}{a numeric vector representing expression of ENSG00000077274.}
#'   \item{ENSG00000101888}{a numeric vector representing expression of ENSG00000101888.}
#'   \item{ENSG00000115548}{a numeric vector representing expression of ENSG00000115548.}
#'   \item{ENSG00000122884}{a numeric vector representing expression of ENSG00000122884.}
#'   \item{ENSG00000125430}{a numeric vector representing expression of ENSG00000125430.}
#'   \item{ENSG00000131370}{a numeric vector representing expression of ENSG00000131370.}
#'   \item{ENSG00000135443}{a numeric vector representing expression of ENSG00000135443.}
#'   \item{ENSG00000136457}{a numeric vector representing expression of ENSG00000136457.}
#'   \item{ENSG00000138398}{a numeric vector representing expression of ENSG00000138398.}
#'   \item{ENSG00000150636}{a numeric vector representing expression of ENSG00000150636.}
#'   \item{ENSG00000161277}{a numeric vector representing expression of ENSG00000161277.}
#'   \item{ENSG00000163510}{a numeric vector representing expression of ENSG00000163510.}
#'   \item{ENSG00000164485}{a numeric vector representing expression of ENSG00000164485.}
#'   \item{ENSG00000164651}{a numeric vector representing expression of ENSG00000164651.}
#'   \item{ENSG00000166091}{a numeric vector representing expression of ENSG00000166091.}
#'   \item{ENSG00000166342}{a numeric vector representing expression of ENSG00000166342.}
#'   \item{ENSG00000171121}{a numeric vector representing expression of ENSG00000171121.}
#'   \item{ENSG00000177173}{a numeric vector representing expression of ENSG00000177173.}
#'   \item{ENSG00000180229}{a numeric vector representing expression of ENSG00000180229.}
#'   \item{ENSG00000188817}{a numeric vector representing expression of ENSG00000188817.}
#'   \item{ENSG00000197360}{a numeric vector representing expression of ENSG00000197360.}
#'   \item{ENSG00000203601}{a numeric vector representing expression of ENSG00000203601.}
#'   \item{ENSG00000225449}{a numeric vector representing expression of ENSG00000225449.}
#'   \item{ENSG00000230201}{a numeric vector representing expression of ENSG00000230201.}
#'   \item{ENSG00000233996}{a numeric vector representing expression of ENSG00000233996.}
#'   \item{ENSG00000236138}{a numeric vector representing expression of ENSG00000236138.}
#'   \item{ENSG00000236819}{a numeric vector representing expression of ENSG00000236819.}
#'   \item{ENSG00000250602}{a numeric vector representing expression of ENSG00000250602.}
#'   \item{ENSG00000253923}{a numeric vector representing expression of ENSG00000253923.}
#'   \item{ENSG00000256980}{a numeric vector representing expression of ENSG00000256980.}
#'   \item{ENSG00000259083}{a numeric vector representing expression of ENSG00000259083.}
#'   \item{ENSG00000259134}{a numeric vector representing expression of ENSG00000259134.}
#'   \item{ENSG00000260484}{a numeric vector representing expression of ENSG00000260484.}
#'   \item{ENSG00000263612}{a numeric vector representing expression of ENSG00000263612.}
#'   \item{ENSG00000264049}{a numeric vector representing expression of ENSG00000264049.}
#'   \item{ENSG00000264954}{a numeric vector representing expression of ENSG00000264954.}
#'   \item{ENSG00000265579}{a numeric vector representing expression of ENSG00000265579.}
#'   \item{ENSG00000271711}{a numeric vector representing expression of ENSG00000271711.}
#'   \item{ENSG00000272071}{a numeric vector representing expression of ENSG00000272071.}
#'   \item{ENSG00000276517}{a numeric vector representing expression of ENSG00000276517.}
#' }
#' @source TCGAbiolinks TCGA-CESC
#' @examples
#' data("cesc")
#' head(cesc)
#' @keywords datasets
"cesc"