A small human PBMC multiome example dataset

A near-balanced 500-cell subset of the PBMC multiome dataset from SeuratData, containing paired RNA and peaks assays for package examples and tests. The dataset keeps approximately equal numbers of cells for each major PBMC cell type, retains the top 12000 accessible peaks by total counts within the selected cells, and keeps RNA genes with at least 10 total counts in the subset (12405 genes). When available, the peaks assay stores a compact hg38 gene annotation derived from EnsDb.Hsapiens.v86 and collapsed to the longest transcript per gene.

Format

A Seurat object with 12405 RNA genes, 12000 peaks, and 500 cells.

Source

Derived from the PBMC multiome reference data distributed through SeuratData / pbmcMultiome.SeuratData.

Examples

if (interactive()) {
  thisutils::check_r("satijalab/seurat-data")
  InstallData <- thisutils::get_namespace_fun("SeuratData", "InstallData")
  InstallData("pbmcMultiome")
  data(pbmcMultiome)
  pbmcMultiome <- UpdateSeuratObject(pbmcMultiome)

  set.seed(98)
  n_per_type <- ceiling(500 / length(unique(pbmcMultiome$cell_type)))
  cells_sub <- unlist(
    lapply(
      split(colnames(pbmcMultiome), pbmcMultiome$cell_type),
      function(x) sample(x, size = min(n_per_type, length(x)))
    ),
    use.names = FALSE
  )
  pbmcmultiome_sub <- subset(pbmcMultiome, cells = cells_sub)

  peak_counts <- GetAssayData5(pbmcmultiome_sub, assay = "peaks", layer = "counts")
  peaks_keep <- names(sort(Matrix::rowSums(peak_counts), decreasing = TRUE))[seq_len(12000)]
  rna_counts <- GetAssayData5(pbmcmultiome_sub, assay = "RNA", layer = "counts")
  genes_keep <- names(Matrix::rowSums(rna_counts))[Matrix::rowSums(rna_counts) >= 10]
  pbmcmultiome_sub <- subset(pbmcmultiome_sub, features = c(genes_keep, peaks_keep))

  use_data <- thisutils::get_namespace_fun("usethis", "use_data")
  use_data(
    pbmcmultiome_sub,
    compress = "xz",
    overwrite = TRUE
  )
}