A data compendium for genetic profiles - by Hanqing Zhao
Now it is capable of:
① Downloading data from all the branches under TCGA portal.
② Rendering them into MultiAssayExperiments and saving them to local as R data objects.
Cautions:
① Some data will be unavailable if you run this code on Windows 10/11, because Windows 10/11 has set a maximum limit to the length of filepaths. As a result, it complains when extracting some specific files.
② If you want to run it on Windows 10/11, set the destination path as SHORT as possible.
③ Make sure you have enough space (at least 8 GB recommended) for downloading and extracting process.
I have organized my code into a project like this. It seems more decent :)
Now it is capable of:
① Downloading TCGA-BRCA, TCGA-COAD, TCGA-PAAD data.
② Extracting required part of data (experiments, pdata, etc.)
Something in construction:
① The function to fill our experiments and pdata into a MultiAssayExperiment.