Questions about S4

[julia-wrobel]

• How do we look at an object and see what's in it? Like for example I want to do FPCA but I might have multiple summaries calculated and I want to know what they are named so I know what to extract
• For key slot in S4 object, what do we do when we have multiple images per subject? We will need both a subject id and an image id. Can we talk through this?
• Can we also talk more generally about how to extract information from the S4 object? This isn't super intuitive to me
• How do I add/edit variables to the object?
• What do we do about images with an NA for the summary function? We need a way to deal with this.
• This isn't really an S4 question, but it seems like somewhere we calculated a subset of the lung data and are using that instead. Where did that happen?
• How do I add slot name of mFPCA for multilevel FPCA?

[ACSoupir]

1. should be able to run summary or just calling the object.
2. there are 2 key slots in the S4 object - one for sample and one for subject. This was implemented in previous push of object. summary now uses both of these to report number of subjects and unique samples.
3. Sure. Happy to add more functions to make this easier
4. Tricky because S4 objects are made in a way that specifically prevents users from openly manipulating what is in it (each slot has a class that must be respected). This makes sure that whatever is in the object works with down-stream functions that are expecting specific data formats.
5. The issue of NAs will be something that you will have to decide what to do with. spatialTIME keeps all radii, marker, sample combinations and fills with NA that is later then treated as a separate class (missing), but suspect this is easier when looking at a single radius rather than a curve (unless a function can be converted to classes?).
6. Depends on step that you are referring to. Is data(lung) a subset of data? I have 116 subjects and 180 samples (reported from summary) and 209,391 rows. In the data creation R file clean_lung_data.R it filters to only "Tumor"?
7. Will have to do this likely in the object creation class of mxfda_object.R. Which raises the question of if you want the PCA/Cox slots to have a class other than list. Entirely up to you.