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
https://github.com/DavisLaboratory/standR/blob/62dff22c9da7f54f48e0a4cbb061ebeb514fd458/R/batchCorrection.R#L237C5-L237C86
G'day,
Just a thought - with the call to
geomxBatchCorrectionwithinfindBestKcurrently the assay is being selected as the function default forgeomxBatchCorrection(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 :)