[Bioc-devel] Updates to SingleCellExperiment class structure - no action required

Aaron Lun |n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Sun Feb 16 09:50:47 CET 2020

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.



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