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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.