MarioniLab/archive-cydar

normalizeBatch target batch?

Closed this issue · 3 comments

Is there any way to choose a "target batch" when applying the normalizeBatch function, so as to align landmarks to a particular batch? And is it possible to supply any of the flowStats implementation arguments such as bandwidth for density estimation?
Thanks

LTLA commented

Yes, this could definitely be done. I'll see if I can add these features over the coming week.

Thank you! One additional suggestion--the ability to choose a subset of markers in the flowSet/matrix to be normalized would save some extra code.

LTLA commented
  1. You can now specify the target batch via target.
  2. You can now pass arguments to flowStats::warpSet via ....
  3. You can now specify the markers of interest via markers=.

However, two things to note:

  • I haven't tested any of these features (even if they are syntatically valid, or if the package builds!) because flowWorkspace is not installing on my machine - I will need to check why.
  • Commits will be to https://github.com/MarioniLab/cydar, this repository is now archived.