Parse the oncoprint free-text mutation column

Usage

zhn_parse_oncoprint(df, remove_negative = TRUE)

Arguments

df

Cohort data frame from zhn_read_cohort().

remove_negative

Logical; drop "negativ/kein Nachweis" entries (default TRUE).

Value

A data frame with one row per (patient, alteration) pair: patient_label, diagnose_label, alteration, alteration_class, alteration_raw, oncoprint_mutation. Empty input returns a 0-row tibble with this column set.

Details

Splits the free-text mutation column into per-alteration rows, classifies each entry via zhn_alteration_type(), and flags genuine mutations for the oncoprint tile plot.

Unlike the legacy v5 implementation, this function does not call shiny::validate() – packaged functions must work outside Shiny. If the required source column is missing, the function raises a cli::cli_abort so the server layer can wrap the message with validate(need(...)).

See also

Other parsers: zhn_parse_cytogenetics(), zhn_prepare_diagnostic_blocks(), zhn_prepare_therapy_blocks()