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jishnu-lab / SLIDE

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The vignette had a few minor errors #33

Closed NiklausZZZ closed 3 months ago

NiklausZZZ commented 3 months ago

Vignettes have a lot mistakes, such as: image

And, image

The vignettes may be not well understood for users.

TranscriptionFactory commented 3 months ago

The first is an easy fix (thanks for catching the typo!), but please clarify the issue with the second (the yaml file path is used to load the yaml parameters, which are then checked for correct inputs). Thanks for pointing these out @NiklausZZZ !

NiklausZZZ commented 3 months ago

Does the description here match the picture? I am a lot confused. Any explanation would be greatly appreciated! image

NiklausZZZ commented 3 months ago

The first is an easy fix (thanks for catching the typo!), but please clarify the issue with the second (the yaml file path is used to load the yaml parameters, which are then checked for correct inputs). Thanks for pointing these out @NiklausZZZ !

Thank you for your quick reply! Indeed, yaml_path is the directory of yaml file:

checkDataParams(yaml_path)
Error in input_params$x_path : $ operator is invalid for atomic vectors

Using checkDataParams(input_params) will work: image

TranscriptionFactory commented 3 months ago

Does the description here match the picture? I am a lot confused. Any explanation would be greatly appreciated! image

explanation has been generalized and updated

NiklausZZZ commented 3 months ago

Thanks!

TranscriptionFactory commented 3 months ago

Thanks @NiklausZZZ - Please let us know if you find anything else!

NiklausZZZ commented 3 months ago

By the way, does SLIDE require the expression matrix (which is easy to understand) to be combined with phenotypic information (e.g., treatment response, age, gender, mutation)? It seems that phenotypic information is necessary.

TranscriptionFactory commented 3 months ago

Yes, SLIDE requires a single response label for regression/classification. Agreed re: additional phenotypic info necessary - currently, we do not integrate multiple responses but that is a great idea for next steps!