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AlexsLemonade / scpcaTools

BSD 3-Clause "New" or "Revised" License
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[BUG] Matrix.utils has been removed from CRAN #134

Closed jashapiro closed 2 years ago

jashapiro commented 2 years ago

Describe the bug The removal of Matrix.utils from CRAN means we need to remove it as a dependency from our code, as the package will no longer build

The only place that we use the function directly is in collapse_intron_counts(), which is in turn called by read_alevin() and read_kallisto()

For read_alevin(), we should be able to use on fishpond to perform the same functions for reading and collapsing directly.

I don't think kallisto stores ambiguous counts separately, so we should be able to simply drop the intron reads and not use the Matrix.utils::aggregate.Matrix() function at all.

We can probably perform this step within the read_kallisto() function itself and remove the collapse_intron_counts() function completely.

jashapiro commented 2 years ago

An alternative solution may be to replace Matrix.utils::aggregate with DelayedArray::rowsum() which should have a similar function.

I think moving to fishpond is still a good idea, but may not be required at this stage.