[BioC] Generalized edgeR functions

[Davide Cittaro]

Hello list, 
In another experiment I'm analyzing read counts on different sets of genomic intervals. I would like to apply edgeR functions to normalize read counts but... Since my sets of intervals do not necessarily overlap, I thought I can extract overlapping intervals (which, by the way, are a considerable part of the whole dataset) and use those to estimate TMM parameters and dispersion. Subsequently I would like to apply the same metrics to the original counts, this time including all intervals. Assuming this makes any sense to you, how would you suggest to proceed?

Thanks

d