Ramos_MultiAssayExperiment.Rmd about biocworkshops

[LiNk-NY]

Thanks Levi @lwaldron. I've modified your comment to create a checklist.

[LiNk-NY]

Hey Levi, @lwaldron
Is there something I left out of the workshop?
Thanks,
MR

[lwaldron]

Yes @LiNk-NY , some suggestions - and I'll include as many as you can finish by Weds in the CSAMA workshop this Thursday. I can help out with it between now and then too.

• additional text in the captions to explain the SE, MAE, and RE figures
• use suppressPackageStartupMessages()
• section Working with RaggedExperiment: more introductory text to explain what it is, when and how you use RE
  • note similarities with SummarizedExperiment
• example(GRangesList) - can you shorten this? The output is very long
• *Assay functions - introductory paragraph needed
• Working with MultiAssayExperiment - introductory paragraph needed
  • note similarities with SummarizedExperiment - maybe a table showing functions in common, e.g. rows for functions and columns for SE, RE, and MAE, with checkboxes where the function is implemented?
• add the cheat sheet as an image
• for curatedTCGAData(..., dry.run=FALSE), hide ExperimentHub output
• Start TCGAUtils section by doing simplifcation of acc object
• Demo UUID conversion
• Demo filtering and separating by sample type (e.g. 1: solid tumors only, 2: split apart different sample types as different ExperimentList objects)

[lwaldron]

Thanks @LiNk-NY, these are great improvements. Can you expand on this statement in the Rmd?

• Note: Coercion to SummarizedExperiment is possible.

[lwaldron]

The API cheat sheet image does not make it into the bookdown @LiNk-NY

[LiNk-NY]

I fixed this. Thanks.