During the EuroBioc, I just ended up reading through the docs and spotted this potential minor update.
I remember that at the Boston BioC conference, some discussion took place regarding which convenience accessors to keep/deprecate for the SingleCellExperiment class.
I saw that scater currently enables the accessors:
c("exprs", "norm_exprs", "stand_exprs", "fpkm")
While I think it's nice to keep the exprs accessor for backward compatibility to the 'main' assay matrix (i.e., ExpressionSet, SCESet), I saw that in this case it is systematically redirected to the logcounts accessor.
As a user, I would argue that it is more didactic to showcase the more direct logcounts accessor in the help pages and examples, even if the exprs is still offered. Just so that users more clearly know what slot they're accessing. (Alternatively, exprs could throw a warning that it accesses an assay named differently to the function, as it is the only exception).
kevinrue
commented
6 years ago
During the EuroBioc, I just ended up reading through the docs and spotted this potential minor update.
I remember that at the Boston BioC conference, some discussion took place regarding which convenience accessors to keep/deprecate for the
SingleCellExperimentclass. I saw thatscatercurrently enables the accessors:c("exprs", "norm_exprs", "stand_exprs", "fpkm")While I think it's nice to keep the
exprsaccessor for backward compatibility to the 'main' assay matrix (i.e.,ExpressionSet,SCESet), I saw that in this case it is systematically redirected to thelogcountsaccessor. As a user, I would argue that it is more didactic to showcase the more directlogcountsaccessor in the help pages and examples, even if theexprsis still offered. Just so that users more clearly know what slot they're accessing. (Alternatively,exprscould throw a warning that it accesses an assay named differently to the function, as it is the only exception).Dropbox links:
Note that this pull request also includes some automatic RStudio formatting that I didn't bother turn off (mostly trimmed spaces at ends of lines).
Please feel free to decline the pull request, if undesirable. I just thought I'd offer a user's perspective!
Thanks for the hard work!