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add n_assay argument for findBestK #22

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samleenz opened this issue Oct 5, 2023 · 0 comments
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add n_assay argument for findBestK #22

samleenz opened this issue Oct 5, 2023 · 0 comments
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enhancement New feature or request

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@samleenz
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samleenz commented Oct 5, 2023

https://github.com/DavisLaboratory/standR/blob/62dff22c9da7f54f48e0a4cbb061ebeb514fd458/R/batchCorrection.R#L237C5-L237C86

G'day,

Just a thought - with the call to geomxBatchCorrection within findBestK currently the assay is being selected as the function default for geomxBatchCorrection (n_assay = 2) without an option for the user to change this when calling the function. This seems a little risky - as in effect it's assuming that the logcounts assay will always be in the second position.

I think it could be worth adding n_assay as an argument to findBestK that just passes through to the internal batch correction call? Happy to do a pull request for it if you want

Cheers :)

@ningbioinfo ningbioinfo added the enhancement New feature or request label Jan 31, 2024
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