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Examples of how to query the cancer_analysis table and integrate with the phenotypic/clinical data of these participants using the R LabKey API (Rlabkey package) are listed here. We make use of the SQL like syntax to query the tables. You can use RStudio or R in the terminal to run these examples and to do further downstream processing of the data. 


The sample IDs in the somAgg VCFs are the 'tumour_sample_platekey' (e.g. LP3000448-DNA_A09) - not the participant IDs. In order to link between plate-key and participant ID - use the cancer_analysis table. There is one sample per row in this table.