GAMBLR.viz glossary

There are several key concepts underlying the logic behind the GAMBLR.viz package. The main terms are:

• these_samples_metadata: This is a data frame with a set of minimal required columns: patient_id, Tumor_Sample_Barcode, sample_id, seq_type, sex, cohort, and pathology. The columns like sex and cohort can contain NA values but must be present in the metadata. The main purpose of this data frame is to provide a structure for the metadata that is always expected to be available and provides linkage between unique sample identifiers and associated basic metadata values. The columns Tumor_Sample_Barcode and sample_id are expected to share the same values, but are required to be present for direct operation on the outputs of different upstream tools.