Add support for TreeSE

[TuomasBorman]

Issues

• Resolves Support for TreeSE? #346.

Change(s) made

This PR implements support for TreeSummarizedExperiment. This allos the following workflow:

library(mia)
data("Tengeler2020")
tse <- Tengeler2020

tse <- preprocess_data(dataset = tse, outcome_colname = "patient_status")

res <- run_ml(
    tse, "rf", altexp = "preprocessed", assay.type = "preprocessed",
    outcome_colname = "patient_status")

Checklist

(Strikethrough any points that are not applicable.)

• Write unit tests for any new functionality or bug fixes.
• Update docs if there are any API changes:
  • roxygen comments
  • vignettes
• Update NEWS.md if this includes any user-facing changes.
• The check workflow succeeds on your most recent commit. This is always required before the PR can be merged.