Updated to conform to BioC package guidelines - Githubissues

BaderLab / netDx

R package with netDx software and data for examples

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Updated to conform to BioC package guidelines #65

Closed shraddhapai closed 4 years ago

shraddhapai commented 4 years ago

Major changes to conform to BioConductor package guidelines

buildPredictor() takes a MultiAssayExperiment object instead of phenotype data.frame and list for data
Dependence on netDx.examples eliminated and need for that package eliminated. All examples are either now contained in netDx or are pulled from BioConductor (e.g. curatedTCGAData).

Other changes

Master functions no longer write files for users; no sink() calls to create log files. Log files now need to be generated by the user.
system() calls replaced with system2
no set.seed() calls
cat() replaced with message()
Started adding unit tests using testthat
Other miscellaneous changes (e.g. replacing 1..n with seq_len(), replacing class() with

Major pending

Capability to handle CNV/mutation data needs to be built in using the new MultiAssayExperiment format.

shraddhapai commented 4 years ago

All conflicts resolved, BiocCheck runs without errors or warnings.