Convert a MultiAssayExperiment to a ReticulateMuData

Converts each experiment in a MultiAssayExperiment::MultiAssayExperiment() to a Python anndata.AnnData modality, then assembles them into a ReticulateMuData.

Required package

This function requires the MultiAssayExperiment Bioconductor package, which is listed under Suggests. Install it with:

BiocManager::install("MultiAssayExperiment")

Experiment handling

• SummarizedExperiment::SummarizedExperiment and SingleCellExperiment::SingleCellExperiment experiments are converted via sce_to_anndata().

• Experiments of any other type emit a warning() and are skipped.

Sample (column) metadata

The MAE's colData is joined to each modality's obs before building the MuData, so that all per-sample annotations are available globally via mdata$obs once mdata$update() is called.

Usage

mae_to_reticulate_mudata(mae, assay = NULL, ...)

Arguments

mae

A MultiAssayExperiment::MultiAssayExperiment.

assay

Character string or NULL. Name of the assay to use as X for every experiment. If NULL (default) the first available assay is used for each experiment individually.

...

Additional arguments forwarded to sce_to_anndata() for each experiment modality.

Value

A ReticulateMuData wrapping a Python mudata.MuData.

See also

sce_to_reticulate_mudata(), sce_to_anndata(), ReticulateMuData

Examples

if (FALSE) { # \dontrun{
# ---- Tiny MAE with two experiments ----
library(MultiAssayExperiment)
library(SingleCellExperiment)
library(Matrix)
library(S4Vectors)

set.seed(1)
n_samples <- 50
sample_ids <- paste0("sample_", seq_len(n_samples))

rna_mat  <- Matrix::rsparsematrix(200, n_samples, 0.1, repr = "C")
rownames(rna_mat) <- paste0("gene_", seq_len(200))
colnames(rna_mat) <- sample_ids

adt_mat  <- Matrix::rsparsematrix(30, n_samples, 0.4, repr = "C")
rownames(adt_mat) <- paste0("protein_", seq_len(30))
colnames(adt_mat) <- sample_ids

sce_rna  <- SingleCellExperiment(assays = list(counts = rna_mat))
sce_adt  <- SingleCellExperiment(assays = list(counts = adt_mat))

sample_df <- S4Vectors::DataFrame(
  condition = sample(c("ctrl", "treat"), n_samples, TRUE),
  row.names = sample_ids
)

el <- MultiAssayExperiment::ExperimentList(rna = sce_rna, adt = sce_adt)
cl <- MultiAssayExperiment::listToMap(
        setNames(lapply(c("rna","adt"), function(nm) {
          data.frame(primary = sample_ids, colname = sample_ids)
        }), c("rna","adt"))
      )
mae <- MultiAssayExperiment::MultiAssayExperiment(
  experiments = el,
  colData     = sample_df,
  sampleMap   = cl
)

mdata <- mae_to_reticulate_mudata(mae)
print(mdata)
mdata$n_obs()
mdata[["rna"]]
mdata[["adt"]]
} # }