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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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what's the meaning of p_ttest in call.cns file ?I cannot find any description about this value . #697

Open whiffen-cann opened 2 years ago

etal commented 2 years ago

It's the p-value resulting from a 1-sample t-test of that segment's probes's log2 values versus 0.0. https://github.com/etal/cnvkit/blob/master/cnvlib/segmetrics.py#L23

I agree it ought to be documented.

tetedange13 commented 2 years ago

Hi @etal,

I think batch section of documentation can still be improved (probably a lot of CNVkit users go through this subcommand first) => My ideas are: splitting into subsections for clarity + adding examples headers => I will try to prototype this and submit a PR

Also not directly related, but: => In ReadTheDocs, selecting "master" instead of default "stable" (when coming from CNVkit README) does not actually show latest changes made into documentation (such as new details about batch post-processing steps) => Is it an expected behaviour ?

Kind regards, Felix