[Bioc-devel] Updates to SingleCellExperiment class structure - no action required
It sounds to me that the class definition / structure is updated. You should also have an associated updateObject() method to deal with this; that's tradition. Of course, you may already have addressed this and just not written about it in your email. On Sun, Feb 16, 2020 at 3:51 AM Aaron Lun <
infinite.monkeys.with.keyboards at gmail.com> wrote:
Dear list, As of version 1.9.2, the SingleCellExperiment class structure has been updated so that "sizeFactors()<-" will store values in a "sizeFactor" field in the "colData()", rather than the internal metadata. This aims to improve interoperability of the SCE size factors with functions that retrieve information from the column metadata; see GitHub for details. This change occurs under the hood in the "sizeFactors()" getter and setter functions, so no action should be required from users who were already using those functions to manipulate the SCE size factors. Nonetheless, downstream developers should keep an eye on their unit tests as some of the more fragile checks may fail, e.g., if they hard-coded the expected column names of the "colData" of an SCE. Version 1.9.2. also removes a bunch of deprecated functionality from the package, which may cause unrelated failures; though this was pretty esoteric stuff that didn't see a lot of use in the first place. Best, -A
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Best, Kasper [[alternative HTML version deleted]]