Add support for exporting CGH data to MeV

[Nicklas Nordborg]

This is supposed to be straightforward the format is well-defined.

[Nicklas Nordborg]

I am thinking that maybe we should also consider moving the MeV TDMS export out from the core package into this exension. At the same time it would be nice to also fix ​http://base.thep.lu.se/ticket/742 so that both the TDMS and CGH export can build upon a generic export plug-in.

[Nicklas Nordborg]

The text below is from the MeV documentation (​http://expression.washington.edu/mevr/files/MeV_Manual_4_0.pdf). Can anybody confirm if this is what is meant by "the format is well-defined"? If so, which BASE columns corresponds to the pieces of reporter data? I would guess that Probe/Marker --> ExternalID, Probe Chromosome --> Chromosome, but 3 and 4 doesn't seem to have any related reporter column in a standard BASE installation. Do we need to define additional reporter columns as part of the MeV package?

CGH Analyzer allows data to be loaded from one format only. The format includes 4 mandatory columns followed by sample columns. The mandatory columns are:

1. Probe/Marker
   
2. Probe Chromosome,
   
3. Probe Genomic Start in BP,
   
4. Probe Genomic End in BP
   

The mandatory columns are followed by Sample observations where each observation for each probe is the log2 or simple intensity ratio of Cy3 & Cy5. If the observations are not log2 transformed they are done so by the module

[Nicklas Nordborg]

Some more questions:

1. Are the columns tab-separated?
2. Can someone attach an example CGH file to this ticket?

[Nicklas Nordborg]

My best idea so far is to not complicate things too much. I prefer not to force a specific configuration in BASE 2 for the four columns in the CGH file. Instead I think the plug-in should support a configurable "mapping". This can, for example, be done though a regular plug-in configuration that maps the four columns to formulas that can map them to almost any reporter annotation that is desired. The configuration may also include an option if the values should be logged or not.

Comments on this?

Any answers to the questions above? I will start on this next week and need something soon. Or should this ticket be moved to a later release?

[Nicklas Nordborg]

It seems like the information in the documentation is incorrect. In the CGH loader dialog (screenshot) it seems like it needs 5 columns. I also found an example cgh file that I will attach to this ticket.

[Nicklas Nordborg]

MeV CGH loader dialog

[Nicklas Nordborg]

Example CGH file

[Nicklas Nordborg]

(In [1082]) References #212: Add support for exporting CGH data to MeV

The exporter and plug-in is in place. The plug-in is configurable with respect to which reporter annotations to use for 'chromosome', 'start', 'end' and 'description'. Values are logged if the bioassay set uses logged values, otherwise the pure ratios are exported.

[Nicklas Nordborg]

(In [1083]) References #212: Add support for exporting CGH data to MeV

I have changed the GUI a bit to make sure that it can handle both CGH and TDMS files. It is now also possible to generate a new export file directly from the MeV button.

[Nicklas Nordborg]

(In [1086]) References #212: Add support for exporting CGH data to MeV

Fixed a timing issue that could prevent MeV from being started.