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Prepare input data common for all experiments

Source: R/prepare_input.R
prepare_input.MultiAssayExperiment.Rd

Current steps

  • refining nested confounders

  • refining nested identifiers

  • splitting df_ into (per experiment) df_list

Usage

# S3 method for MultiAssayExperiment
prepare_input(
  x,
  nested_confounders = gDRutils::get_SE_identifiers(x[[1]], "barcode"),
  nested_identifiers_l = .get_default_nested_identifiers(x[[1]]),
  raw_data_field = "experiment_raw_data",
  split_data = TRUE,
  ...
)

Arguments

x

MAE object with dose-response data

nested_confounders

Character vector of the nested_confounders for a given assay. nested_keys is character vector of column names to include in the data.tables in the assays of the resulting SummarizedExperiment object. Defaults to the nested_identifiers and nested_confounders if passed through

nested_identifiers_l

list with the nested_identifiers(character vectors) for single-agent and (optionally) for combination data

raw_data_field

metadata field with raw data

split_data

Boolean indicating need of splitting the data into experiment types

...

additional parameters

Value

list of input data