In the PureCN (v 1.14.2) function calculateTangentNormal the tumor fragment counts are denoised creating a sort of "log-ratio" which is then converted to average coverage and this average coverage is used later on to calculate the log-ratio that will be used in the segmentation. Was curious why segmentation isn't done on the denoised fragment counts/log-ratio. Does this have something to do with how the fragment counting is performed?

Thanks!

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin18.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] PureCN_1.14.2

Yes, mostly to keep the API simple and unchanged from older versions.

The average coverage in calculateTangetNormal is set so that the calculateLogRatio function exactly returns the denoised log-ratio. So you should get identical result when you provide runAbsoluteCN the tangent normal (via normal) or the denoised log-ratio (via log.ratio).