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Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
…is: "Correspondance" → "Correspondence" (#792) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Signed-off-by: Daena Rys <rysdaena8@gmail.com>
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| #' By default \code{scater::calculateMDS} keeps only the \code{ntop = 500} | ||
| #' most variable features. When rarefaction is enabled (\code{niter > 0}) the |
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does the R code throw a warning of this if it does not use all features? (if data has more than 500)
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As we have mia::getMDS and mia::addMDS, we could set the default to no filtering. At least, I have not heard that variance filtering is commonly used in MDS in microbiome context (or then authors of papers have not explicitly stated that)
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Yes, I would also set the default to no filtering.
We can show examples on how to add filtering.
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@0xMuluh Can you update the PR based on discussion? |
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Summary of Changes
ntop = Infby default inmia::getMDSandmia::addMDSso that all features are retained before running MDS, avoiding unintended feature filtering in the microbiome context (unlikescater::calculateMDSwhich defaults tontop = 500).R/getMDS.Randman/addMDS.Rddescribing feature retention and how to supply a finitentoporsubset.rowif feature filtering is desired.tests/testthat/test-addMDS.R.Relates to microbiome/OMA#824.