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[hail] add lambda GC calculation #6498

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merged 4 commits into from Jun 28, 2019

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@konradjk
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commented Jun 27, 2019

Also added table_source since I couldn't find it - let me know if I missed it

@konradjk konradjk changed the title Adding lambda GC calculation [hail] add lambda GC calculation Jun 27, 2019

med_chisq = hl.agg.approx_quantiles(chisq, 0.5)
else:
med_chisq = hl.median(hl.agg.collect(chisq))
return t.aggregate(med_chisq / hl.qchisqtail(0.5, 1))

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@tpoterba

tpoterba Jun 27, 2019

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can we separate the bit that generates the agg expression out into a separate private function? We have an open feature request to print the lambda GC in hl.plot.qq

addressed

oops

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add to docs rst file(s)

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commented Jun 27, 2019

add to genetics.rst

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commented Jun 27, 2019

also add experimental note since this is untested

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Note
----
This method is experimental.

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@tpoterba

tpoterba Jun 27, 2019

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oops sorry this is what I meant:

    .. include:: ../_templates/experimental.rst

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@konradjk

konradjk Jun 27, 2019

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nifty!

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@danking danking merged commit fe8e543 into hail-is:master Jun 28, 2019

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@konradjk konradjk deleted the konradjk:lambdagc branch Jun 28, 2019

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