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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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error for AESPCA and SuperPCA examples #47

Closed lxw391 closed 5 years ago

lxw391 commented 5 years ago

I got an error when I tried to test AESPCA, see attached error_for_AESPCA.docx

gabrielodom commented 5 years ago

Similar error for SuperPCA_pVals(). Looking into it.

gabrielodom commented 5 years ago

In this example, we create an OmicsSurv object directly with the CreateOmicsSurv() function, rather than the user-facing CreateOmics() function. The error is because the validity of the assay data and pathway collection objects are checked in the CreateOmics() wrapper, while assuming that these objects have already been checked before any calls to the CreateOmics*() functions. We probably need to update that example, but the bug remains. I need to move validity checking for pathway collections to the CreateOmics*() functions.

gabrielodom commented 5 years ago

Problem: less of a code issue and more of an input issue.

Possible solutions: a. change the CreateOmics*() functions to check and clean the incoming objects (they are currently checked and cleaned in CreateOmics()), OR b. update the examples and help files for the CreateOmics*() functions to point the users back to the CreateOmics() wrapper

Implemented solution: I've removed all mentions of the CreateOmics*() functions from the help files. All help hyperlinks now point to the CreateOmics() wrapper.