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thierrygosselin / radiator

RADseq Data Exploration, Manipulation and Visualization using R
https://thierrygosselin.github.io/radiator/
GNU General Public License v3.0
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Default permutation method in genomic_converter() is null, not "rf" #4

Closed IdoBar closed 7 years ago

IdoBar commented 7 years ago

According to the genomic_convereter() documentation, the default method for imputation is "rf", while in fact it is NULL. It caused me some confusion trying to understand where the imputed results are.

IdoBar commented 7 years ago

Seemed to be fixed in the recent version (v0.0.4)

IdoBar commented 7 years ago

Still appears that way in the detailed imputation.method help:

Default: imputation.method = "rf".

thierrygosselin commented 7 years ago

I see the problem, it's reusing the imputation module For it to work seamlessly I used the rf as default. However, for radiator::genomic_converter I don't want to use it by default, And the problem is that i'm using @inheritParams radiator_imputations_module so that I don't have to write a new @param description to avoid repetition. This is already a problem of circular dependencies... I've extracted the imputation module and made grur. But grur needs radiator to import different genomic file format. So to circumvent the problem I had to include the imputation module of grur inside radiator as an internal function not available for users.

I'll figure out a way to fix this in the doc.

Thanks for reporting this.

thierrygosselin commented 7 years ago

Ok I have workaround the problem. The next version will fix this.