MidarExperiment dataset object • midar

The MidarExperiment object is the main data container used in the MiDAR workflow. It holds all the experimental and processed data and metadata, as well as details of the applied processing steps and the current status of the data.

Most MiDAR functions take an MidarExperiment object as input. Functions that process or update the data return a modified MidarExperiment object as output, allowing it to be used in subsequent functions. You can create and process multiple MidarExperiment objects independently within the same script.

Creating a MidarExperiment object

First the {midar} package is loaded and then we create a new MidarExperiment object.

library(midar)
myexp <- MidarExperiment()

At any time we can obtain a summary on the status of the myexp object using the print() function.

print(myexp)
#> Warning: Unknown or uninitialised column: `feature_id`.

Using MidarExperiment objects

myexp <- MidarExperiment()
myexp <- data_load_example(myexp, 1)
myexp <- normalize_by_istd(myexp)
myexp <- save_dataset_csv(myexp, 
                          "mydata.csv", 
                          variable = "norm_intensity", 
                          filter_data = FALSE)

You can also use MidarExperiment objects in an R pipe chain. This allows you to chain multiple functions together, making your code more streamlined and easier to read while clearly indicating the flow of your processing workflow.

myexp <- myexp |> 
  MidarExperiment() |>
  data_load_example(1) |>
  normalize_by_istd() |>
  save_dataset_csv(myexp, 
                   "mydata.csv", 
                   variable = "norm_intensity", 
                   filter_data = FALSE)

Multiple MidarExperiment objects can be created and processed independently within the same script.

myexp_panel_1 <- data_load_example(myexp, 1)
myexp_panel_2 <- data_load_example(myexp, 1)

Accessing data and metadata

Use specific functions to access data and metadata stored in the MidarExperiment object, rather than directly accessing the object slots. TODO

myexp <- MidarExperiment()
myexp <- data_load_example(myexp, 1)
print(midar::get_analyticaldata(myexp))

Saving and Reading MidarExperiment objects

myexp <- MidarExperiment()
myexp <- data_load_example(myexp, 1)
saveRDS(myexp, file = "myexp-midar.rds", compress = TRUE)
my_saved_exp <- readRDS(file = "myexp-midar.rds")
print(my_saved_exp)