Construct a MultiAssayExperiment

Usage

mae_create(experiments, col_data, sample_map = NULL)

Arguments

experiments: A named list or ExperimentList of experiment leaves.
col_data: Primary sample metadata with unique row names.
sample_map: Optional explicit MAE sample map. When omitted, experiment column names must map directly to primary sample names.

Value

A MultiAssayExperiment::MultiAssayExperiment.

Examples

counts <- matrix(
  1:6,
  nrow = 3,
  dimnames = list(paste0("gene", 1:3), c("sample1", "sample2"))
)
samples <- data.frame(
  condition = c("control", "treated"),
  row.names = colnames(counts)
)
rna <- mae_create_experiment(counts, samples)
mae_create(list(rna = rna), samples)
#> A MultiAssayExperiment object of 1 listed
#>  experiment with a user-defined name and respective class.
#>  Containing an ExperimentList class object of length 1:
#>  [1] rna: SummarizedExperiment with 3 rows and 2 columns
#> Functionality:
#>  experiments() - obtain the ExperimentList instance
#>  colData() - the primary/phenotype DataFrame
#>  sampleMap() - the sample coordination DataFrame
#>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
#>  *Format() - convert into a long or wide DataFrame
#>  assays() - convert ExperimentList to a SimpleList of matrices
#>  exportClass() - save data to flat files