Export and add clinical data to cBioPortal dataset — cbp_add

This should be run in an existing dataset package root.

Usage

cbp_add_clinical(clinical_data, ref_map, verbose = TRUE)

Arguments

clinical_data: Clinical table query.
ref_map: YAML file specifying the mapping of (NF) clinical metadata to cBioPortal model. See details.
verbose: Whether to provide informative messages throughout.

Details

Clinical data are mapped and exported according to a reference mapping. Also reformatting of PATIENT_ID, SAMPLE_ID to contain only letters, numbers, points, underscores, hyphens; in Nextflow processing any spaces gets replaced with underscores so that's the default here. Does not check for missing samples, as final validation via cBioPortal tool is still expected for that.