Prepare survival data from clinical and cytogenetic data

Constructs a data frame suitable for survival analysis from GDC clinical data. Uses `days_to_death` for deceased patients and `days_to_last_follow_up` for censored (alive) patients. Merges with cytogenetic risk groups when available.

Usage

prepare_survival_data(clinical_data, cyto_file = NULL)

Arguments

clinical_data

Cleaned clinical data frame (from clean_clinical_data)

cyto_file

Path to cytogenetic parquet file (from extract_cytogenetic_data), or NULL to skip cytogenetic integration

Value

Data frame with columns: patient_id, time_days, status (0=censored, 1=dead), age_years, gender, iss_stage, risk_group, plus individual cytogenetic markers

See also

Other survival: extract_risk_table(), plot_forest(), plot_km(), run_cox_regression(), run_kaplan_meier(), run_km_by_expression(), run_km_by_markers()