id summary reporter owner description type status priority milestone component resolution keywords cc 1418 Implement support for methylation data Nicklas Nordborg Nicklas Nordborg "This ticket is about importing (EPIC) methylation data from tumor DNA samples. It is somewhat similar to the !OncoArray SNP (see #1346) data in the structure. The starting point is DNA items in BASE. We need to make sure that there are aliquots created that represents the amount taken from the DNA item. Typical name will be something like `1234567.1.l.d.aX` (where X may be missing or a number). The samples sheets that we have only have the `1234567` as identifier so we need to map this first. The DNA aliquot should be linked to `PhysicalBioAssay` item representing the actual EPIC chip that was used. It ~~might~~ is be possible to re-use the `BeadChip` suptype for this with but with new value for the `BeadChipType` annotation (eg. `Epic850K`). ~~The other alternative is to use a new subtype (eg. `EpicChip`).~~ This item also need the `BeadChipID` annotation. The `BeadChipID` allows us to find the data files related to the chip, since they are all contained in a single sub-directory. Each chip has 8 locations which should be linked to the 8 DNA aliquots used on the chip. The DNA aliquots need to have this information as annotations (`R01C01`...`R08C01`). Scanning of the chip is represented by a !DerivedBioAssay `Scan` item. Dates, Scanner ID, etc. can be extracted from the data we have and should be imported as annotations or linked Hardware items. The `DataFilesFolder` annotation will point to a folder with the scan data. We will need the *.idat files in the next step. The scan will produce one pair of *.idat files for each of the 8 samples on the chip. We will represent this as 8 child !DerivedBioAssay items with a new subtype `Methylation`. The *.idat files are are stored in the `` using the existing naming convention (eg. `../12/1234567.1/l.d.mty`). **Downstream analysis** We want to do some analysis that produces beta-values. This will be part of another ticket. **Wizards** See #1419 for a wizard that calculate beta-values. " task closed major Reggie v4.41 net.sf.basedb.reggie fixed