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Store molecule counts in rowData(altExp(sce)) #169

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alanocallaghan opened this issue Mar 27, 2020 · 2 comments
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Store molecule counts in rowData(altExp(sce)) #169

alanocallaghan opened this issue Mar 27, 2020 · 2 comments

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@alanocallaghan
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Related to #133
@alanocallaghan alanocallaghan mentioned this issue May 21, 2020
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@alanocallaghan
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Also this error message:

          "More than one 'altExp' provided; only one allowed. \n
          'altExp' must contain observations for spike-in genes. \n"

is kind of unnecessary. It'd be better to enforce that they're called "spike-ins" or have the altExpName as an argument. However I'm fine leaving it as is

@alanocallaghan
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Also enforcing 2 columns only is a bit odd, better to just ensure that a column name is present ("Molecules" maybe)

alanocallaghan added a commit that referenced this issue Sep 9, 2020
@alanocallaghan
Use rowData(altExp(x)) for spike concs, work towards #175 and #169
0d7558c
alanocallaghan added a commit that referenced this issue Sep 24, 2020
@alanocallaghan
version 2.1.7 (2020-09-24)
ba9630d 
- Bugfix in format method for ResultVG class.
- For `BASiCS_PlotDE`, if only one plot is produced, the plot is returned as
  a bare ggplot object rather than using `cowplot::plot_grid`
- Added `EpsilonThreshold` argument for `BASiCS_DetectHVG` and `BASiCS_DetectLVG`.
  This uses a threshold on epsilon values to identify LVGs and HVGs.
  Also adds a `MinESS` argument to `BASiCS_DetectHVG` and `BASiCS_DetectLVG`.
- Deprecated `newBASiCS_Data` and the `format` methods for Results classes.
  For the latter, use `as.data.frame` instead.
- Improved documentation for BASiCS_ResultVG class
- `BASiCS_MCMC` now computes and stores ESS as an attribute of parameter
  matrices when sampling has completed.
- Make use of Parameter argument consistent across several methods, where Param
  and Which were used before.
- Extended BASiCS_DiagPlot to enable other diagnostic measures
- Moved to store molecule counts in `rowData(altExp(sce))` rather than `metadata(sce)`
- Remove dependency to KernSmooth
- Set some values to NA if they relate to genes captured in < 2 cells
- Add option to exclude spike-ins in `BASiCS_DenoisedCounts`.
  Also use a slightly more principled calculation internally.
- See issues #182, #39, #91, #169, #181, #178, #202, #190, #173
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@alanocallaghan