Improve examples

[TuomasBorman]

Hello,

some of the examples in OMA are too complex. The examples should be clear enough without unnecessary complexity because it might a) prevent readers to get interested on the framework, and b) make harder for readers to troubleshoot possible problems in their code

• [x] 1. Cite to Bioconductor if the package can be found from there https://microbiome.github.io/OMA/docs/devel/pages/miaverse.html#other-relevant-packages

Check these examples

• [x] 2. Check if importBIOM has option for polishing the names.

The rowData() polishing step is little bit off-scope. I think it would be better to remove it.

https://microbiome.github.io/OMA/docs/devel/pages/import.html#standard-data-formats

• [x] 3. From all examples, replace %>% with |>

Unifies the code.

• [x] 4. Paragraph unclear

https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#subset-by-sample-column-wise

"This chapter covers various basic techniques for preparing data for subsequent analysis. These include subsetting, splitting, and modifying data, as well as converting data to a data.frame through melting and merging multiple SummarizedExperiment objects. See Chapter 3 for basics of TreeSE."

-->

The list could be improved. For instance, it seems that converting to df requires merging multiple SEs which is not the case.

• [x] 5. Remove since other examples do not have this kind of package listing

https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#sec-treese_subsetting

Load:

mia
dplyr
knitr
data GlobalPatterns

• [x] 6. "Note" block should be in the end of the example.

Remve the paragraph starting with "As a sanity check,..."

https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#subset-by-sample-column-wise

• [x] 7.

Paragraph "Several criteria can be used to subset by sample:" does not make sense (at least like this.) It could be removed. The subsetting is dependant on research question and listing these like this does not seem right.

• [x] 8. Combine 6.1.2 and 6.1.3

These are actually referring to same example.

https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#subset-by-feature-row-wise

• [x] 9. Add link to agglomeration chapter

In agglomerateByRanks, add link to agglomerations chapter

https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#splitting

• [ ] 10. How to add data to assay

Create an example that adds new sample

https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#sec-add-or-modify-data

• [x] 11. Remove package from function call

https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#melting-data

mia::meltSE --> meltSE

• [x] 12. Explain why splitting might be useful

We might want to split the data, if we want to analyze the data for instance from different cohorts separately. https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#splitting

• [x] 13. Explain why we want to add data

https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#sec-add-or-modify-data

• [x] 14 Create a note block

Create a note from this

https://microbiome.github.io/OMA/docs/devel/pages/wrangling.html#sec-treese_subsetting