search

jernst98 / ChromHMM

GNU General Public License v3.0
74 stars 18 forks source link

"flankwidthcontrol" in Preprocess #25

Closed zhangnan0107 closed 4 years ago

zhangnan0107 commented 4 years ago

The ChromHMM manual said that flankwidthcontrol is used to compute average control counts for all bins within x-w and x+w for the xth bin, however, the sum of counts rather than average counts is calculated in the code (windowSumGrid method in Preprocessing class, see the following picture).

Manual: image

Code: image

So I am wondering which one is actually used? It seems that average value is more reasonable. Maybe the mean counts is computed somewhere else?

Thanks Nan

jernst98 commented 4 years ago

They end up being equivalent for determining the binarization threshold based on how the values are used in determineMarkThresholdsFromBinnedDataArrayAgainstControl

Best, -Jason