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Input MultiAssayExperiment data in a teal application

NEST CoreDev

2022-04-20

including-mae-data-in-teal.Rmd

MultiAssayExperiment data

MultiAssayExperiment offers a data structure for representing and analyzing multi-omics experiments: a biological analysis approach utilizing multiple types of observations, such as DNA mutations and abundance of RNA and proteins, in the same biological specimens.

You can read more about MultiAssayExperiment data here.

Example application

The example below represents an application including MultiAssayExperiment data.

library(teal)
utils::data(miniACC, package = "MultiAssayExperiment")

mae_d <- dataset("MAE", miniACC, metadata = list(type = "example"))

app <- init(
  data = teal_data(mae_d),
  modules = example_module()
)

if (interactive()) {
  shinyApp(app$ui, app$server)
}

The filter panel supports MAE data out of the box, but teal itself does not guarantee that any module will work with MAE data the same way it works with other types of data (e.g. ADaM) because MAE has a unique structure that needs to be considered when developing a module. The package teal.modules.hermes has been specifically developed for the analysis of MAE data.

For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the teal.data package.