Methylation data freeze tasks

[fsvarn]

We need to harmonize the clinical data so that the methylation data freeze can go forward. Here is a checklist of things that we need to do:

• [x] Check methylation uuids against the RNA/DNA uuids to make sure there is no overlap. Contact Laila with list of conflicting aliquots if there are any (Taylor)
• [x] Correct "-5MC-" aliquots in the files table (and possibly the methylation matrix) and fix conflicting uuids (Laila)
• [x] Fix conflicting case level information (Fred)
• [x] Make a list of conflicting surgery rows for CWRU and HF clinical data files (Taylor)
• [x] Choose which fields to update if any for conflicting rows (Fred and Taylor)
• [x] Update conflicting row fields (Taylor)
• [x] Update MGMT methylation columns for HK (and possibly prior pubs?) (Taylor)
• [x] Merge case table
• [x] Merge samples table
• [x] Merge aliquots table
• [x] Merge files table
• [x] Merge clinical surgeries table
• [x] Fix received_alkylating_agent column in clinical data

[fpbarthel]

Are you guys cross checking the inferred genotypes from the methylation arrays to the DNA sequencing data?

[fsvarn]

The methylation array column is just relating to MGMT methylation based on the arrays the methylation group ran.