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predictSex no longer works as wateRmelon predictSex has been replaced by estimateSex #14

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johnomics opened this issue Apr 6, 2022 · 2 comments
Open

predictSex no longer works as wateRmelon predictSex has been replaced by estimateSex #14

johnomics opened this issue Apr 6, 2022 · 2 comments

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@johnomics
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bigmelon's predictSex function relies on wateRmelon's predictSex (see gdsnclass_methods.R L1109), but wateRmelon's predictSex function was replaced by estimateSex (schalkwyk/wateRmelon@d82639d) so bigmelon's function no longer works.

A workaround is to use wateRmelon's estimateSex on the betas directly:

library(bigmelon)
gfile <- openfn.gds("dataset.gds")
estimated_sexes <- estimateSex(betas(gfile)[,])
closefn.gds(gfile)
@TJGorrie
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Sorry for the huge delay - life got in the way. Thank you for opening the issue up. Will get on it.

@johnomics
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No problem, I know how it goes, and this was easy to work around. Thanks for looking into this. Bigmelon is a great package, thanks for developing it.

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@johnomics @TJGorrie