Implement support for methylation data

[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 <project-archive> 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

We do not plan to implement wizards for this. Reggie will simply create/define item types, annotation types, etc. that are needed. Batch importers will be used to import data and batch exporters will be used to get data into scripts that are manually created.

[Nicklas Nordborg]

In 6865:

References #1418: Implement support for methylation data

Added DNA/Methylation to the Pipeline annotation, Epic850K to the BeadChipType annotation and a new Methylation subtype for derived bioassays.