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BaderLab / Tempora

Pathway-based trajectory inference method for time-series scRNAseq data
MIT License
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GSVA parallel.sz argument throws error #2

Closed innesbre closed 4 years ago

innesbre commented 4 years ago

Leaving CalculatePWProfiles(...,parallel.sz=NULL) (the default) causes an error when method is set to GSVA because it expects an integer (NULL breaks the logical arguments they use to evaluate number of cores to assign). Not sure how to make GSVA not operate in parallel, since setting it to FALSE yielded the same behaviour as setting it to 0 (GSVA default) - all available cores were used.

thinh-tran commented 4 years ago

You can set parallel.sz=1 to stop GSVA from doing the analysis in parallel (this is now the default). I have updated the documentation of the CalculatePWProfiles function and change the default from NULL to 1. Thank you for catching this!