Thanks, Michael. Wonderful. On Tue, Aug 25, 2009 at 10:27 PM, Michael Lawrence <[email protected]>wrote:
> Well, it would help if we had a few more details, but to calculate the > number of reads within each 1kb window of the genome, it's something like: > > library(BSgenome.Hsapiens.UCSC.hg18) # assuming human > widths <- rep(1000, seqlengths(Hsapiens)[1]/1000) > # assuming 'cov' is a coverage Rle for chr1 > windows <- successiveViews(cov, widths) > x <- viewSums(windows)/1000 > > That should get you the numbers you need for that scatterplot. > > Michael > > On Tue, Aug 25, 2009 at 7:11 PM, Bogdan Tanasa <[email protected]> wrote: > >> Hi everyone, >> >> please could you let me know if there is any way to represent in a 2D plot >> the number of ChIP-seq tags / 1kb genome window for 2 experiments ? eg : >> >> on X axis : the number of tags / 1kb window for protein 1; >> on Y axis : the number of tags / 1kb window for protein 2; >> >> thanks very much. >> >> -- bogdan >> >> [[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
