MultiAssayExperiment.TCGA

MultiAssayExperiment.TCGA is the pipeline package for building and uploading MultiAssayExperiment datasets from the GDAC Firehose pipeline as obtained from RTCGAToolbox.

There are several steps to rebuild datasets for 33 cancer types.

Generally, users should use the packaged product of the pipeline:

curatedTCGAData

For those looking to rebuild the pipeline, there are several steps that need to be followed:

0. Create all data directories required (dataDirectories)
1. Obtain all clinical and assay data from RTCGAToolbox (saveRTCGAdata)
2. Introduce additional clinical variables to all clinical datasets
3. Download and integrate subtype curation data from Dropbox
4. Generate and serialize data maps, providing relationships between samples and patients
5. Update metadata and upload to ExperimentHub (buildMultiAssayExperiments)

These functions can be found in the data-raw, inst/scripts, and R folders.

NOTE. Include AWS CLI authentication credentials in the ~/.Renviron file. It should include three key:value pairs, AWS_SESSION_TOKEN, AWS_SECRET_ACCESS_KEY, and AWS_ACCESS_KEY_ID