Perform ACME calculation
This function performs the moving window chi-square calculation. It is written in C, so is quite fast.
do.aGFF.calc(x, window, thresh)
An integer value, representing the number of basepairs to include in the windowed chi-square calculation
The quantile of the data distribution for each sample that will be used to classify a probe as positive
A window size on the order of 2-3 times the average size of fragments from sonication, digestion, etc. and containing at least 8-10 probes is the recommended size. Larger size windows are probably more sensitive, but obviously reduce the accuracy with which boundaries of signal can be called.
A threshold of between 0.9 and 0.99 seems empirically to be adequate. If one plots the histogram of data values and there is an obvious better choice (such as a bimodal distribution, with one peak representing enrichment), a more data-driven approach may yield better results.
An object of class
Sean Davis <email@example.com>
1 2 3