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RGLab / MAST

Tools and methods for analysis of single cell assay data in R
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Prefix melt with reshape2:: #122

Closed combiz closed 4 years ago

combiz commented 4 years ago

There are a series of warnings resulting from melt(llrt), melt(lfc), and melt(coefAndCI) which are found in ZlmFit.R and ZlmFit-logFC.R . Can be resolved with reshape2:: prefixes or perhaps reworked with the newer pivot_longer? Thanks

In melt(llrt) :
  The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(llrt). In the next version, this warning will become an error.
gfinak commented 4 years ago

Appreciate the heads-up. We'll make the fixes.

jacobpwagner commented 4 years ago

Done in 94dc2619f289e4b3438f880ac874d7c290e3ac52. For now I opted to just prefix the reshape2 namespace. tidyr::pivot_longer won't work out of the box because it can't handle multidimensional arrays. It's not hard to rework the methods to use pivot_longer or even base methods, but MAST still adds a method to the reshape2::melt generic for SingleCellAssay, so it doesn't yet make sense to completely detach it until that is renamed.