Support multiple files at once

[lbeltrame]

Currently you have to load every file individually and do all the analyses one at a time. It would be nice to do things like limma, where from a single target file you'd be able to load all the files together and batch process them.

My use case: several (10+) CGH arrays produced in the group I work in, which I'd like to batch-process.

[fredcommo]

I guess by 'a single target' you mean a single target folder, correct ?

That's a great suggestion. However, since rCGH produces objects and not just data frames, I think providing in-batch function would lead to make some arbitrary decisions regarding the output formats.

A simple solution to run multiple files would be to embed the main rCGH functions - read, adjustSignal, EMnormalize, segmentCGH - in one workflow function, and to loop over all the files. You'd then have multiple choices for saving/exporting each result: as individual objects or all by-gene tables merged in one single dataset, or both.