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shishenyxx / DeepMosaic

DeepMosaic is a deep-learning-based mosaic single nucleotide classification tool without the need of matched control information.
https://www.nature.com/articles/s41587-022-01559-w
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Condition for "extra_mosaic_filters" #35

Closed duct317 closed 3 months ago

duct317 commented 3 months ago

Hi, I was looking at the prediction code and noticed the condition for extra_mosaic_filters filter here: https://github.com/shishenyxx/DeepMosaic/blob/a6a2f451c28147ace821522762dcf07028d414b0/deepmosaic/makePrediction.py#L102-L103

Shouldn’t the condition (lower_CIs >= 0.5) & (upper_CIs < 0.5) always evaluate to false? It seems contradictory since the lower bound of the confidence interval (CI) should not be greater than the upper bound.

Thank you, Duc

shishenyxx commented 3 months ago

Thank you for picking up the bug, Duc!

Should be upper_CIs >= 0.5 and lower_CIs < 0.5

This line was only used for the x-y pseudo autosomal regions (0.00087 of the genome) it won't affect the majority of the predictions. I fixed that and will release a new version.

Best,

Xiaoxu

duct317 commented 3 months ago

Thank you for the reply.

Duc