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waldronlab / MultiAssayExperiment

Bioconductor package for management of multi-assay data
https://waldronlab.io/MultiAssayExperiment/
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Expand documentation of setters and getters #281

Closed llrs closed 4 years ago

llrs commented 4 years ago

I was having some problems with colData and sampleMap and tried reading the documentation. However, I couldn't find there enough information to solve my problem:

?sampleMap leads to the document MultiAssayExperiment-methods.Rd created by R/MultiAssayExperiment-class.R, R/MultiAssayExperiment-methods.R. It says "value: See details", but there isn't a details section. On the Setters section is mentioned that "a DataFrame object relating samples to biological units and assays". But it doesn't explain that the value must have row names that match the primary key of colData, or how long, which columns should be provided.

A more detailed description of the required conditions and formats for these functions to work will be appreciated. Thanks.

PS: Note that this is not detailed on the MultiAssayExperiment-class page

LiNk-NY commented 4 years ago

There is information about the value type in the method signature, e.g., MultiAssayExperiment,DataFrame. I have added more information in the documentation. I would also refer you to the prepMultiAssay function which would help you find any issues with your data labels. Thanks. -MR

llrs commented 4 years ago

Great! Thanks for the reference, I missed it and just now I see it on the vignette. A link on "See Also" section of the MultiAssayExperiment-class might help to discover it from the help pages.