Develop revert pre balance train #29
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Plot AUPRC with thresholds. Added in a for loop to go through the input chroms for benchmarking. Will output a unique file per chromosome AUPRC.
Removed average signal from analysis and tested training and prediction.
Develop is9
This code should allow for either a BED file input for predictions or the names of the chromosomes you want to predict in.
#19 Whole genome prediction, ROI prediction, and chromosome predictions
max-combine code added
There was an error for whole-genome prediction that caused it to crash after chromosome9 because it was not in the expected order of the header of the bigwig file. I fixed the chrom sizes file and sorted it by number correctly. I also removed the sorted() function that ordered the chromosomes incorrectly.
The call peaks function ended up producing the wrong peaks for our models because it as subtracting a 1 from the start position. This has been fixed.
Fixed a bug in peak calling
When we import the data for prediction we are not replacing None values with 0. This is different than the approach that we used with bulk data analysis. The reason we want to do this is because we are import None values and I am not sure how that changes our predictions.
Added an optional argument to the parser for setting the min and max values you want to normalize the scores to.
Fix the bugs with string - int type error
added 4 commits
May 17, 2021 15:01
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Revert changes from Balanced Training to PCPC_Random Training.