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gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
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CreateOmics() fails for region collections #89

Open gabrielodom opened 4 years ago

gabrielodom commented 4 years ago

When we create a pathway collection for CpGs, the names of the "sets" will be regions instead of pathways. I need to go through the pathwayPCA code to see where I hard-coded pathway.

Fix necessary for @lxw391 work

gabrielodom commented 4 years ago

Error message:

Error in names(pwyColl_ls$pathways) <- pathNames : 
  attempt to set an attribute on NULL
gabrielodom commented 4 years ago

@lxw391 , this fix will take quite some time, as we use the the $pathways syntax abundantly in our code. How badly do we want to be able to call the first element "regions" instead of "pathways"? Is "pathways" not generic enough?

For now, I'm going to edit the pathway collections to change their label from regions to pathways, just to continue testing the code.