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
