PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
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sruddy17 • 0
@sruddy17-14320
Last seen 11 months ago

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

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Entering edit mode
@markusriester-9875
Last seen 28 days ago

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).