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Assay should default to counts in SummarizedExperiment objects #5

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drisso opened this issue May 16, 2020 · 1 comment
Open
2 of 3 tasks

Assay should default to counts in SummarizedExperiment objects #5

drisso opened this issue May 16, 2020 · 1 comment

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@drisso
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drisso commented May 16, 2020 •
edited by willtownes

It seems to be the standard to store raw counts in the counts assay, so it would be a better default than the current (assay = 1).

  • Feature Selection
  • GLMPCA
  • Null residuals
@LTLA LTLA mentioned this issue Jun 1, 2020
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@willtownes
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willtownes commented Aug 26, 2020 •
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this is now implemented for feature selection. f130f73

@willtownes willtownes changed the title Suggetion: assay should default to counts in SummarizedExperiment objects Assay should default to counts in SummarizedExperiment objects Aug 26, 2020
willtownes added a commit that referenced this issue Aug 26, 2020
@willtownes
simplify GLMPCA method definitions and set default assay to 'counts' …
d1c8824 
…addresses #5 . Moves the L argument in front of assay since it is a required positional argument by glmpca
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@willtownes @drisso