Development #68
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Development #68
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By default RATs will now report only the dtu_freq from the bootstraps. The other bootstrap result fields are omitted, allowing RATs to no longer keep in memory 5 columns per iteration for later processing. This improves memory footprint and scalability from linear to constant with regards to number of bootstraps.
This reverts commit ddf3b77.
This reverts commit 4af1b1c.
In case things fall apart again.
Leaving shiny as optional due to size. Most of the other optionals were negligible and nothing is gained from making the package more complex to document and maintain.
Removed some word-y bits, tidied up some phrasing. Also made most code executable again, to reduce chance of forgetting to update the examples if in the future the syntax of a function changes.
bulk of bootstrapping code placed inside function
next failure is in test 5
ToC works better in HTML. And avoids the pdflatex dependency that is a pain.
Only remaining warning is a mismatch in R versions under which packages were built.
R CHECK is all clear now
Going forward, mean is the default behaviour. User can choose to use sum instead, as in the old behaviour.
I couldn't remember what scenarios the old data represented. So I remade them from scratch, trying to be less cryptic.
still work to be done
All tests pass in R4.0.3
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Main reason to pull is the fix of a bug preventing the import of Kallisto data when the number of samples in the two conditions is not equal.
A number of other changes from the stalled conversion to bioconductor standards are coming a long with that fix. The unit tests are passing, so it is probably safe to release and use.