[Bioc-devel] SummarizedExperiments
Thanks for all the additional methods. I still miss seqlevels, seqlengths, genome Below,
On Wed, Sep 12, 2012 at 3:33 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
On 09/12/2012 12:15 PM, Kasper Daniel Hansen wrote:
One thing I have in my package that I find indispensable is combine and (my own) combineList. The later for combining > 2 objects, which has a lot of possibilities for speed up especially if (very common) all the objects have the same rowData, as opposed to Reduce(combine, LIST).. Usecase: you need to add additional samples to your SummarizedExperiment.
I found it difficult in Biobase to write combine methods for eSet, where you're really requiring a lot from the user (about the phenoData / featureData structured in the same way) or going through contortions to make it the same in a reasonable-but-ad-hoc way (e.g., when two columns are factors with the same set of levels but encoded differently). Maybe the effort required is proportional to the utility of the function provided... I'll give it some more thought.
In the abstract case it is hard to imagine combining different SummarizedExperiments. My usecase is almost always "additional samples from the same experiment", and for that situation it is a lot easier to imagine combining it. You still need to check that the granges are similar (and if not, expand some of the assayData with zeroes or NA's), since the new samples may have coverage in locations not assayed earlier. Clearly factors are hard to handle and I assume there are other hard to handle cases. Nevertheless, I find such a function incredibly useful. I think it is entirely ok to assume that the user knows what (s)he is doing. Kasper