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niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
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What is the mean by "discrimination_value_ML" in the somatic output file #19

Open deb0612 opened 3 years ago

deb0612 commented 3 years ago

Dear sir, What is the meaning of "discrimination_value_ML" in output.test_somatic file? and how does it generate? Another question Is the location column in the output.test_somatic file refer to the position of first base of left_flank sequence or the position of repeat_unit_bases?

owehann commented 3 years ago

Hi Thanks for your interest in MSIsensor2. "Discrimination_value_ML" refers to the determination value given by machine learning methods, and sites whose values greater than 0.5 are generally regarded as unstable. Besides, location column refers to the position of "repeat_unit_bases".

tzvi909 commented 1 year ago

Hi, where can one find the machine learning methods you're using to discriminate between an MSI site and a naturally occuring simple repeat in the ref genome? I'm guessing if you're using the coefficient of determination (R^2) as a discrimination value it's some kind of regression model right?

ZhaoDanOnGitHub commented 1 year ago

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