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Bioconductor / OrchestratingSingleCellAnalysis

Content for the OSCA Book.
http://bioconductor.org/books/devel/OSCA/
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A couple of more text fixes #9

Closed csoneson closed 4 years ago

csoneson commented 4 years ago

Addresses most of the points mentioned in #7

LTLA commented 4 years ago

Now, say we have a different dimensionality reduction approach which has not yet been implemented with SingleCellExperiment objects in mind. For example, let's say we want to explicitly use the umap() function as implemented in the uwot package.

Seems like the original text was wrong, we have runUMAP that does exactly this.

csoneson commented 4 years ago

Seems like the original text was wrong, we have runUMAP that does exactly this.

Yes; my attempt was to make a minimal change that would still illustrate the general approach, but remove the statement about scater using umap. But it's of course true that uwot::umap has already been implemented with SingleCellExperiment objects in mind...

LTLA commented 4 years ago

@robertamezquita merge and fix re. my comment above.

csoneson commented 4 years ago

Re: chosen in the data integration chapter: it is mentioned on lines 209 and 223, but never initialized and never used. Fix depends on whether the intention was to use a subset of the genes or not - if yes, I guess these two mentions should be changed to chosen.hvgs and an argument subset.row provided on lines 217-218; if not, those text lines should be modified.