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lima1 / PureCN

Copy number calling and variant classification using targeted short read sequencing
https://bioconductor.org/packages/devel/bioc/html/PureCN.html
Artistic License 2.0
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Seems forgotten assignmet operator #356

Closed sleyn closed 6 months ago

sleyn commented 6 months ago

Hello!

I was looking on implementation of tangent normalization and found an operaton without an assignment operator: fcnts_std_final - median(apply(fcnts_std_final,2,median)) in createNormalDatabase.R.

It looks like it should be fcnts_std_final <- fcnts_std_final - median(apply(fcnts_std_final,2,median))

https://github.com/lima1/PureCN/blob/c7fddf087671538c995cd665b85a5d354a3aa9ef/R/createNormalDatabase.R#L217C5-L217C62

lima1 commented 6 months ago

Oh. That's an important part of the code base. Will have a look. I benchmarked against GATK4 back then and got identical results, so hopefully that value is expected to be 0 most of the time. Thanks again!

lima1 commented 6 months ago

Was indeed close to 0 in all of my datasets. Should be fine now though.