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cognoma / cancer-data

TCGA data acquisition and processing for Project Cognoma
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Add recurrent solid & metastatic samples #47

Closed dhimmel closed 6 years ago

dhimmel commented 6 years ago

But still include only a single sample per patient.

Closes https://github.com/cognoma/cancer-data/issues/46

dhimmel commented 6 years ago

Still have one more commit which fixes a bug with counts in diseases.tsv.

dhimmel commented 6 years ago

Still have one more commit which fixes a bug with counts in diseases.tsv.

Here is the commit that I was thinking of adding: https://github.com/dhimmel/cancer-data/commit/8f4f23143f5857a76862c286bb07b1246abbcf80. It changes diseases.tsv so counts for n_expression_samples and n_mutation_samples are for all sample types (not just the ones we filter to). However, I am not actually sure this is useful. This could be counting matched normal tissue, which we don't really want for diseases.tsv, so I think we should leave it as is.