Modify Cell Names and Combine Datasets

Extracts expression data from a MultiAssayExperiment object, modifies cell identifiers by appending a unique experiment index (e.g., "-m1", "-m2", etc.), and merges the datasets into a single object.

Usage

earlyj(input_list, rowg = TRUE)

Arguments

input_list

A MultiAssayExperiment object containing expression data from multiple experiments or conditions.

rowg

Logical. If TRUE (default), genes are assumed to be rows and cells columns. If FALSE, matrices are transposed before renaming and combining.

Value

A MultiAssayExperiment object containing a single merged experiment with modified (unique) cell names.

Details

For matrices, this function optionally transposes the input before combining. For Seurat and SingleCellExperiment objects, only features (genes) common across all input datasets are retained before merging. The cell names are suffixed with "-m1", "-m2", etc., according to their original list position. The result is returned as a MultiAssayExperiment with a single merged experiment.

Examples

data(toy_counts)

merged_mae <- earlyj(toy_counts)
merged_mae
#> A MultiAssayExperiment object of 1 listed
#>  experiment with a user-defined name and respective class.
#>  Containing an ExperimentList class object of length 1:
#>  [1] merged: SingleCellExperiment with 35 rows and 120 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