dimalvovs
dimalvovs
- add a test that fails on empty patterMarkers - make it pass by rewriting the method for threshold='all'
Related to #102. It is not explicitly defined how the patternMarkers() threshold needs to operate, this function needs to be refactored. - document modes (thresholds) - document and review simplicityGENES()...
The codebase for CoGAPS has become hard to navigate as more and more functionality was added with time. Let's add comments to the most essential and hard to understand parts...
Can we get saving and starting from Checkpoints reinitialized for CoGAPS? Otherwise given the execution speed the results are lost if runtime is longer than the time limit for some...
There used to be a semi-supervised [CoGAPS version](https://github.com/FertigLab/CoGAPS-bioc/blob/master/R/gapsMapRun.R) that seem to have disappeared. ##Can it be brought back? - [ ] create a plan - [ ] https://github.com/FertigLab/CoGAPS/issues/76 ##And make...
it has been reported that the default number of patters is suboptimal and confusing. Is there a way to set it in a smarter way than simply choosing 7 ([currently...
When CoGAPS is run in distributed mode, one of the matrix gets fixed, thus making standard deviation absent from the output. Lets think of ways to being it back.
There are tests in the https://github.com/FertigLab/CoGAPS/tree/master/src/cpp_tests, but we seem to have lost the knowledge of how up to date those are and do those work at all. Are the tests...
Here is a comment left by someone [in the code](https://vscode.dev/github/FertigLab/CoGAPS/blob/master/R/class-CogapsResult.R#L80-L81), let's treat it properly here. ``` # TODO: fix this check for semisupervised case # if (sum(object@featureLoadings < 0) >...
- fix outdated catch version; - reverse the test compilation condition (make ON default, used to be OFF); - add mechanics of calling cpp tests from within R; - add...