Hello everybody, Is there any Bioconductor tool designed to analyse/visualise the shape OF A SET of ChIP-seq peaks?
Now the same question but with more words: It is simple to visualise the shape of a single peak by computing the coverage along the chromosome. The human eye can immediately identify a peak's centre and its tails. Thus, one can tell peak width, peak sharpness and, if it exists, bi-modality. A violin graph for instance --see library(lattice)-- is a one step solution for its descriptive statistics A more complex problem is to try to compute a consensus shape out of 30000 ChIP peaks. I reckon that the peaks should be somehow centred and then the tags consolidated relative to each centre. A violin graph of the consolidated set would then finish up the task. I wonder if a Bioconductor tool for this purpose already exists or I will have to code it myself. Thank you, Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
