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PeteHaitch / DelayedMatrixStats

A port of the matrixStats API to work with DelayedMatrix objects from the DelayedArray package
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matrixStats 1.0.0: Breaking changes #91

Closed HenrikBengtsson closed 1 year ago

HenrikBengtsson commented 1 year ago

Hello, matrixStats 1.0.0 is now on CRAN (as 2023-06-02). It comes with the following significant changes:

  1. useNames = TRUE is the new default for all functions.

  2. colQuantiles() and rowQuantiles() only sets quantile percentage names when useNames = TRUE, to align with how argument names of stats::quantile() works in base R. Previously, useNames = FALSE also had such names attributes.

PeteHaitch commented 1 year ago

Thanks Henrik. I'll await how we resolve this in https://github.com/Bioconductor/MatrixGenerics/issues/31 before updating DelayedMatrixStats.

LTLA commented 1 year ago

Looks like you need to propagate useNames = useNames at

https://github.com/PeteHaitch/DelayedMatrixStats/blob/166420114b974ca628ca900994717785ffbbdf99/R/utils.R#L316

Otherwise, user-provided overrides aren't respected when the dispatcher decides it can skip block processing.

PeteHaitch commented 1 year ago

@LTLA Won't the user-provided useNames be passed via ...?

LTLA commented 1 year ago

No, because .smart_seed_dispatcher() has an explicit useNames argument, so it gets pulled out of the ....

PeteHaitch commented 1 year ago

Addressed as part of https://github.com/PeteHaitch/DelayedMatrixStats/pull/96