CreateOmics() fails for region collections

[gabrielodom]

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]

Error message:

Error in names(pwyColl_ls$pathways) <- pathNames : 
  attempt to set an attribute on NULL

[gabrielodom]

@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.