This short post introducds the gdc_clinical() function recently added to the GenomicDataCommons package.
The rich data model at the NCI Genomic Data Commons (GDC) includes clinical and biospecimen details. A recently added feature to the NCI GDC Data Portal is the ability to download tab-delimited files or JSON files for clinical and biospecimen details of samples. The details available in these simplified formats are also available via the GDC API.
The NCI Genomic Data Commons (GDC) now contains the authoritative source of data from The Cancer Genome Atlas (TCGA) as well as several other projects of import to the cancer research community. One of the available assays produces somatic variant calls, formally identified by comparing tumor reads and normal reads to identify variants relative to the human reference genome that are not present in the normal genome of the patient.
Introduction The NCI Genomic Data Commons (GDC) is a reboot of the approach that NCI uses to manage and expose genomic and associated clinical and experimental metadata. I have been working on a Bioconductor package that interfaces with the GDC API to provide search and data retrieval from within R.
testing In the first of what will likely be a set of use cases for the GenomicDataCommons, I am going to address a question that came up on twitter from @sleight82