livnatje/DIALOGUE

allowed labels for `DIALOGUE.run(pheno=)`

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yugeji commented

Hello,

In the documentation for DIALOGUE.run, it specifies that the label passed into pheno should be binary. Is there a particular reason for this? Would it be possible to specify a continuous label/how might this affect DIALOGUE?

Thank you very much!

livnatje commented

Hi Yugeji,

You are right, the phenotype can also be multi-class or continuous. We will be releasing a new version of DIALOGUE soon, which will support these type of phenotypes as well.

Thanks,
Livnat

abs51295 commented

Hey @livnatje thanks for the package! I had the same question: Does pheno have to be binary still? Also, does it just affect the plotting part or even the computation part of DIALOGUE . I see pheno being used in DIALOGUE3 function, but I am not sure what pheno means there. Is it just celltype or the pathology column from the test dataset?

Thanks

livnatje commented

@abs51295 and @yugeji a new set of functions was added to test the association of MCPs with multi-class/continuous features. Use DIALOGUE.pheno.multiclass(R,pheno) with the pheno input being a string denoting the name of the feature you'd like to test. This can now be multi-class or continuous.

Let me know if you have any questions or encounter any issues. Thanks