Converts the wide clinical export distributed with legacy TCGA data
releases (column names of the form
patient.age_at_initial_pathologic_diagnosis) into an analysis-ready
tibble with follow-up times in days. Three column layouts are supported:
the generic layout, the oesophageal carcinoma layout ("esca"), and the
stomach adenocarcinoma layout ("stad").
Usage
tcga_clinical(clin, cancer = c("default", "esca", "stad"))
Arguments
- clin
Data frame with one row per patient in the legacy TCGA layout.
- cancer
Column layout: "default", "esca" (the historical
ESAC = TRUE variant), or "stad".
Value
A tibble with the patient barcode, age, sex, stage, node status,
T stage, disease-free survival, relapse and death status with their
times, and, where available, chemotherapy and response. The "esca"
layout additionally returns the histological subtype and tumour
location.