Hi list, I would like to seek your advice with this. Here I have a GRangesList and a GappedAlignments objects (an alignment to the genome). For each GRanges (with length 1) in the GRangesList, I would like to do a sliding window on its ranges and count reads from each window. So far I wasn't able to find an efficient way to do this. My problem is similar to this one: http://permalink.gmane.org/gmane.science.biology.informatics.conductor /34431. But looping over the GRangesList (and using countOverlaps inside the loop) takes significant time. Thanks for any suggestions. Best, Jason

Hi Jason, On 11-08-02 07:46 PM, Jason Lu wrote: > Hi list, > > I would like to seek your advice with this. > Here I have a GRangesList and a GappedAlignments objects (an alignment > to the genome). For each GRanges (with length 1) in the GRangesList, ^^^^^^^^^^^^^^^^^^^^^^^ Are you saying each GRanges in your GRangesList object contains only 1 range? Wouldn't then make sense to unlist your GRangesList object to work instead with 1 big GRanges object? It's just a little bit easier to work with a GRanges object than with a GRangesList object. > I would like to do a sliding window on its ranges and count reads from > each window. So far I wasn't able to find an efficient way to do this. Assuming you are now using a GRanges object (gr0) instead of a GRangesList object. Have you tried to loop over the sliding window instead of looping over the ranges in 'gr0'? This will probably lead to a much smaller loop as the nb of times you move the sliding window is likely to be much smaller than the nb of ranges in 'gr0'. To be a little bit more explicit: for each position of the sliding window, generate a GRanges object 'gr' that is of the same length as 'gr0' and where each range represents the current position of the window. Then do 'countOverlaps()' inside the loop. If you use sapply() for the looping, you will end up with a matrix where the nb of cols is the nb of positions of the sliding window. > My problem is similar to this one: > http://permalink.gmane.org/gmane.science.biology.informatics.conduct or/34431. > But looping over the GRangesList (and using countOverlaps inside the > loop) takes significant time. If you show us the code you are using for doing this then we'll know exactly what you are trying to do. Cheers, H. > > Thanks for any suggestions. > > Best, > > Jason > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319