Checking my understanding of option -d

[qserenali]

I saw this explanation and therefore used the full chromosome length instead of 500 for option -d, but the job ran forever. I checked with two of my colleagues who were able to get the jobs completed and they were using the default 500. -d D start:stop:stepsize of distance. e.g. 15:500:50 means check acf at distances of:[15, 65, 115, 165, 215, 265, 315, 365, 415, 465]

python ~/cpv-0.48/cpv/acf.py -d 1:500:50 -c 5 DMR.baseline.sorted.10-22.bed > DMR.baseline.acf.10-22.txt

DMR.baseline.sorted indeed contain the results for the full chromosome. could someone confirm if the second position shall be the length of the full chromosome for the EWAS analysis? if yes, what is the trick for getting it to complete the run, e.g. increase step size?

Many thanks!

[brentp]

500 is a good value. You definitely don't want to use the full chromosome length. It uses something like a sliding window. Hope that helps.