Warning message for reference SCT model counts correction#10329
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mccormickceci wants to merge 1 commit intomainfrom
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Warning message for reference SCT model counts correction#10329mccormickceci wants to merge 1 commit intomainfrom
mccormickceci wants to merge 1 commit intomainfrom
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Pull request overview
Adds user-facing notification in SCTransform.Assay when a reference.SCT.model is supplied, clarifying that UMI count correction is disabled in that mode.
Changes:
- Emit a note when
reference.SCT.modelis provided anddo.correct.umiis forced toFALSE. - Preserve existing behavior of disabling centering/count correction under reference-model usage.
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| message( | ||
| "NOTE:A reference SCT model was provided, therefore counts are NOT corrected (Regardless of argument passed to do.correct.umi)" | ||
| ) |
| do.correct.umi <- FALSE | ||
| do.center <- FALSE | ||
| message( | ||
| "NOTE:A reference SCT model was provided, therefore counts are NOT corrected (Regardless of argument passed to do.correct.umi)" |
…r counts will not be corrected
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@mccormickceci Thanks for the PR! Can you use warning instead of message? You can also remove the "NOTE:" prefix in the warning text.
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Adding a warning message so that users know if they use a reference SCT model we will hard set do.correct.umi to FALSE. We do this since count correction across models is not statistically sound, but we will send a message so that users know their counts will not be corrected.