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FunctionLab / ExPecto

predicting expression effects of human genome variants ab initio from sequence
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Regarding log fold change and predict.py description #1

Closed jeffmylife closed 6 years ago

jeffmylife commented 6 years ago

Hey, the paper mentioned that the variant expression effect prediction is measured by the log(fold change) but I cannot find any log transformations in either chromatin.py or predict.py. I do see in predict.py @line106 there is a standard difference (a-b), not a log fold change.
Am I missing something?

Also, the predict.py description at the top is the same as chromatin.py.

Thanks

jzthree commented 6 years ago

The expression levels are always represented by log-transformed values, therefore all predictions are already in log scale and difference of predictions means log fold change.

Thanks for pointing out the issue in the script description! Fixed now.