Extract cytogenetic markers from clinical data

Parses clinical data from GDC to extract translocation and copy number alteration status. GDC clinical data includes FISH results for standard myeloma cytogenetic markers.

Usage

extract_cytogenetic_data(clinical_dir)

Arguments

clinical_dir

Path to clinical data directory (from download_clinical_data)

Value

Path to saved cytogenetic parquet file

See also

Other cytogenetics: calculate_cooccurrence(), compute_riss(), plot_cooccurrence_heatmap(), plot_cytogenetic_oncoprint(), plot_expression_by_subtype(), summarize_cytogenetics()

Examples

if (FALSE) { # \dontrun{
cyto_file <- extract_cytogenetic_data("data/raw/clinical")
cyto <- arrow::read_parquet(cyto_file)
} # }