See functions like viewMaxs, viewWhichMaxs, viewRangeMaxs... On Tue, Jun 29, 2010 at 5:58 AM, Daniela Drechsel < [email protected]> wrote:
> Hello, > > I'd like to identify the peak summit for each peak in a list of ChIPseq > peaks. I've been using IRanges/Genomic Ranges & Rsamtools to read in the > BAM > file with mapped reads, seperated reads according to '+' and '-' > strand-mappings ( & dropped unmapped reads). > I have a predefined list of peak regions that I'm interested in, so I only > take the reads that map to these regions. > > x=BAM_data[BAM_data %in% Peak_regions] > x_views=views(coverage(x), Peak_regions) > > which gives me an Rle looking like this > > start end width > [1] 3114398 3114591 194 [0 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 > 5 > 5 5 5 5 5 5 5 5 5 5 5 5 5 ...] > [2] 3198876 3199070 195 [0 0 0 0 0 0 0 0 0 0 3 3 3 3 3 3 3 3 3 3 3 3 3 3 > 3 > 3 3 3 3 3 3 3 0 0 0 0 0 0 ...] > > Does anybody have some advice on what is the best way to access the > coverage > data in this object and find the maximum value/summit? > > Many thanks!! > Daniela > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
