% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data-documentation.R
\docType{data}
\name{ovarian}
\alias{ovarian}
\title{Semi-synthesised TCGA Ovarian Cancer Dataset}
\format{
A data frame with 357 rows (patients) and 1007 columns:
\itemize{
\item \strong{OS_time}: Numeric. Observed survival time in days (simulated).
\item \strong{OS_event}: Integer. Event indicator (simulated).
1 = event observed, 0 = right-censored.
\item \strong{treatment}: Integer. Simulated treatment assignment.
1 = carboplatin, 0 = cisplatin. Driven primarily by
\code{year_of_diagnosis} as an instrumental variable
(cisplatin era pre-~2000, carboplatin after).
\item \strong{age}: Integer. Age at initial pathologic diagnosis in years.
\item \strong{figo_stage}: Integer. FIGO stage coded as 2 = Stage II,
3 = Stage III, 4 = Stage IV.
\item \strong{tumor_grade}: Integer. Histologic tumor grade coded as
2 = G2, 3 = G3, 4 = G4. Rows with GX (unknown grade) were
excluded.
\item \strong{year_of_diagnosis}: Integer. Year of initial pathologic diagnosis
(approx. 1992--2013). Used as an instrumental variable for
treatment assignment in the DGP.
\item \strong{right_time, left_time}: Numeric. Interval-censoring bounds
derived from the simulated survival times, suitable for passing
to the package's interval-censored survival interface
(\code{right_time = Inf} for right-censored observations,
\code{left_time == right_time} for exact events).
\item \strong{year_of_diagnosis.1}: Integer. Duplicate of
\code{year_of_diagnosis} left in place from the data-assembly
join; retained for reproducibility and may be ignored.
\item \strong{ENSG...}: Numeric. Log2(TPM + 1) normalised gene expression
levels for 997 Ensembl genes (columns named by versioned Ensembl
gene IDs, e.g. \code{ENSG00000270372.1}). Genes were selected as
the most variable transcripts across TCGA-OV samples, ranked by
median absolute deviation (MAD).
}
}
\source{
\url{https://portal.gdc.cancer.gov/projects/TCGA-OV}
}
\usage{
ovarian
}
\description{
Gene expression and clinical covariates for ovarian cancer patients from
The Cancer Genome Atlas (TCGA-OV), combined with semi-synthetic
survival outcomes and treatment assignment. Real covariates (age,
FIGO stage, tumor grade, gene expression) are retained; survival
times, event indicator, and treatment assignment are simulated from a
known data-generating process so that the true treatment effect is
available for validation (see \code{\link{ovarian_truth}}).
}
\details{
RNA-seq data were downloaded from the GDC portal using the
\code{TCGAbiolinks} package (STAR - Counts workflow). Expression values
were normalised to TPM and log2-transformed as log2(TPM + 1). Genes with
median TPM <= 1 across all samples were removed prior to MAD filtering.
Clinical data were obtained from the BCR Biotab clinical supplement.
Treatment assignment was derived from the drug table
(\code{clinical_drug_ov}), restricted to adjuvant (first-line) treatment
records. Samples were matched between expression and clinical data using
the 12-character TCGA patient barcode.
}
\examples{
data(ovarian)

# Dimensions: patients x (6 clinical + 2000 gene columns)
dim(ovarian)

# Survival outcome
head(ovarian[, c("OS_time", "OS_event", "treatment")])

# KM plot by treatment
if (requireNamespace("survival", quietly = TRUE)) {
  library(survival)
  fit <- survfit(Surv(OS_time, OS_event) ~ treatment, data = ovarian)
  plot(fit, col = c("blue", "red"), xlab = "Time (days)", ylab = "Survival")
  legend("topright", c("Carboplatin", "Cisplatin"), col = c("blue", "red"), lty = 1)
}
}
\references{
Cancer Genome Atlas Research Network (2011). Integrated genomic analyses
of ovarian carcinoma. \emph{Nature}, 474, 609--615.
\doi{10.1038/nature10166}

Colaprico, A. et al. (2016). TCGAbiolinks: an R/Bioconductor package for
integrative analysis with GDC data. \emph{Nucleic Acids Research}, 44(8).
\doi{10.1093/nar/gkv1507}
}
\keyword{datasets}
