Scan chromosomes with a pre-defined window size, comparing scaled ChIP and input tag coutns to see if their ratio exceeds that expected from a Poisson process (normalized for dataset size).
get.broad.enrichment.clusters(signal.data,
control.data,
window.size=1e3,
z.thr=3,
tag.shift=146/2,
background.density.scaling = F,
...)chip.tags, foreground tag vector list
input.tags, background tag vector list
window size to be used for tag counting
Z-score to be used as a significance threshold
number of base pairs by which positive and negative tag coordinates should be shifted towards eachother (half of binding peak separation distance)
If TRUE, regions of significant tag enrichment will be masked out when calculating size ratio of the signal to control datasets (to estimate ratio of the background tag density). If FALSE, the dataset ratio will be equal to the ratio of the number of tags in each dataset.
additional parameters should be the same as those passed
to the find.significantly.enriched.regions
A list of elements corresponding to chromosomes, with each element being an $s/$e/$rv data.frame giving the starting, ending positions and the log2 enrichment estimate for that region.