pdata_stad: Toy STAD Phenotype Data

In IOBR: Immune Oncology Biological Research

Toy STAD Phenotype Data

Description

A data frame containing clinical and pathological annotations for the TCGA stomach adenocarcinoma (STAD) cohort. Each row corresponds to one tumour sample and can be matched to the columns of eset_stad via the ID column. This dataset is typically used together with eset_stad in examples of survival analysis, subgroup comparison and immune deconvolution in the IOBR package.

Usage

data(pdata_stad)

Format

A data frame with one row per TCGA-STAD sample and 8 variables:

ID

Character. TCGA sample barcode, matching the column names of eset_stad.

stage

Factor. Pathological stage (e.g. "Stage_I", "Stage_II", "Stage_III", "Stage_IV").

status

Factor. Vital status at last follow-up ("Alive" or "Dead").

Lauren

Factor. Lauren classification of gastric cancer ("Intestinal", "Diffuse", "Mixed" or NA).

subtype

Factor. Molecular subtype (e.g. "CIN", "EBV", "GS", "MSI").

EBV

Factor. EBV status of the tumour ("Positive" or "Negative").

time

Numeric. Overall survival or follow-up time, typically measured in months.

OS_status

Integer/binary. Overall survival status indicator. (1 = death, 0 = censored)

Examples

data(pdata_stad)
head(pdata_stad)

IOBR documentation built on May 30, 2026, 5:07 p.m.