% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{kircIMR}
\alias{kircIMR}
\title{Reduced TCGA-KIRC Multi-Platform Survival Example}
\format{
A named list with the components:
\describe{
  \item{platforms}{A list of three data frames, `mrna`, `mirna` and
    `methylation`.  Each has an `id` column containing package-internal
    patient labels followed by screened molecular features.}
  \item{covariates}{Clinical covariates with an `id` column: age at initial
    diagnosis, female sex indicator, pathologic stage and histologic grade.}
  \item{outcome}{Alias of `outcome.survival`, for convenience.}
  \item{outcome.survival}{Data frame with `id`, observed survival/follow-up
    time in days and event indicator `status` (1 = deceased, 0 = censored).}
  \item{feature_screening}{Per-platform feature-ranking information and a
    short description of the screening procedure used to create the reduced
    panel.}
  \item{platform_availability}{Patient-level logical matrix indicating which
    of the three platforms are available.}
  \item{subgroup_sizes}{Counts of the non-empty availability subgroups
    induced by the reduced data.}
  \item{model_subgroup_sizes}{The availability subgroups that would be
    modelled under the default real-data illustration threshold
    `ssize = 30`.}
  \item{paper_alignment}{Metadata describing how the reduced example maps to
    the Biometrics KIRC case study.}
  \item{source}{Source URLs and reference metadata.}
}
}
\usage{
kircIMR
}
\description{
A reduced real-data example derived from public UCSC Xena TCGA kidney renal
clear cell carcinoma (KIRC) data, not from controlled-access TCGA/GDC files.
The data set mirrors the multi-platform structure of Chekouo, Stingo, Doecke
and Do (2017): mRNA expression, miRNA expression and DNA methylation are
observed on overlapping but not identical sets of patients, with clinical
covariates and right-censored survival outcome.
}
\details{
The full TCGA source files are not distributed with the package.  Instead,
this object stores a small screened feature panel suitable for examples and
vignette analyses.  Patient identifiers are package-internal labels
(`KIRC001`, `KIRC002`, ...) rather than TCGA barcodes; no barcode mapping is
distributed with the package.  Users should not attempt participant
re-identification or linkage to external resources.  The generating script is
provided in the source repository under `data-raw/make_kircIMR.R`.

The source data are public UCSC Xena TCGA-KIRC sampleMap files:
mRNA expression (`HiSeqV2`), miRNA expression (`miRNA_HiSeq_gene`), DNA
methylation (`HumanMethylation450`) and the KIRC clinical matrix.  Molecular
features are screened with univariable Cox models after basic filtering, and
missing molecular values in the retained panel are median-imputed within
feature.  The full Biometrics analysis used 776 mRNA, 91 miRNA and 729 DNA
methylation features; this package example retains 50, 30 and 50 features,
respectively, to keep examples lightweight.  The package does not distribute
controlled-access TCGA/GDC data or the full Biometrics/Wiley supplementary
data files.
}
\examples{
data("kircIMR", package = "IntegMultiReg")
sapply(kircIMR$platforms, dim)
kircIMR$subgroup_sizes
kircIMR$model_subgroup_sizes
}
\references{
Chekouo T, Stingo FC, Doecke JD, Do K-A (2017). "A Bayesian
Integrative Approach for Multi-Platform Genomic Data: A Kidney Cancer Case
Study." \emph{Biometrics}, \strong{73}(2), 615--624.
\doi{10.1111/biom.12587}

The Cancer Genome Atlas Research Network; National Cancer Institute Genomic
Data Commons; UCSC Xena.
}
\keyword{datasets}
