Build SummarizedExperiment using a Seurat object

Usage

dataset_seurat(
  seurat_obj,
  counts_layer,
  cell_id_col,
  cell_type_col,
  assay = NULL,
  tpm_layer = NULL,
  name = "SimBu_dataset",
  spike_in_col = NULL,
  additional_cols = NULL,
  filter_genes = TRUE,
  variance_cutoff = 0,
  type_abundance_cutoff = 0,
  scale_tpm = TRUE
)

Arguments

seurat_obj: (mandatory) Seurat object with TPM counts
counts_layer: (mandatory) name of assay in Seurat object which contains count data in 'counts' slot
cell_id_col: (mandatory) name of column in Seurat meta.data with unique cell ids
cell_type_col: (mandatory) name of column in Seurat meta.data with cell type name
assay: name of the Seurat objecy assay that should be used. If NULL (default), the currently active assay is used
tpm_layer: name of assay in Seurat object which contains TPM data in 'counts' slot
name: name of the dataset; will be used for new unique IDs of cells
spike_in_col: which column in annotation contains information on spike_in counts, which can be used to re-scale counts; mandatory for spike_in scaling factor in simulation
additional_cols: list of column names in annotation, that should be stored as well in dataset object
filter_genes: boolean, if TRUE, removes all genes with 0 expression over all samples & genes with variance below variance_cutoff
variance_cutoff: numeric, is only applied if filter_genes is TRUE: removes all genes with variance below the chosen cutoff
type_abundance_cutoff: numeric, remove all cells, whose cell-type appears less then the given value. This removes low abundant cell-types
scale_tpm: boolean, if TRUE (default) the cells in tpm_matrix will be scaled to sum up to 1e6

Value

Return a SummarizedExperiment object

Examples

counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE)
tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE)
tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm))

colnames(counts) <- paste0("cell-", rep(1:300))
colnames(tpm) <- paste0("cell-", rep(1:300))
rownames(counts) <- paste0("gene-", rep(1:1000))
rownames(tpm) <- paste0("gene-", rep(1:1000))

annotation <- data.frame(
  "ID" = paste0("cell-", rep(1:300)),
  "cell_type" = c(
    rep("T cells CD4", 50),
    rep("T cells CD8", 50),
    rep("Macrophages", 100),
    rep("NK cells", 10),
    rep("B cells", 70),
    rep("Monocytes", 20)
  ),
  row.names = paste0("cell-", rep(1:300))
)

seurat_obj <- Seurat::CreateSeuratObject(counts = counts, assay = "gene_expression", meta.data = annotation)
SeuratObject::LayerData(seurat_obj, assay = "gene_expression", layer = "data") <- tpm

ds_seurat <- SimBu::dataset_seurat(
  seurat_obj = seurat_obj,
  counts_layer = "counts",
  cell_id_col = "ID",
  cell_type_col = "cell_type",
  tpm_layer = "data",
  name = "seurat_dataset"
)