Hi all, I just joined the list, and was hoping to get some advice about the best way to work with the various classes that deal with genomic range info. I am a postdoc in the Celniker Lab at Lawrence Berkeley National Lab, working on the modENCODE project.
So my question has to do with using various functions that operate on the IRanges level, while keeping my data in RangedData or RangeList objects. I should be able to use rdapply or lapply, but it is not very clear to me when I should use one over another. If I want to calculate the chromosome-by-chromosome coverage for a RangeData object, I can do something like: lapply(ranges(RangedData),coverage, start = 1, end = 1000) but how can I do it for varying starts and ends? Alternatively, is it better to write a function and call it using rdapply? What have you guys been doing for this scenario? Thanks in advance, Jane Landolin _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
