Build SummarizedExperiment using local annotation and count matrix R objects

Usage

dataset(
  annotation,
  count_matrix = NULL,
  tpm_matrix = 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

annotation: (mandatory) dataframe; needs columns 'ID' and 'cell_type'; 'ID' needs to be equal with cell_names in count_matrix
count_matrix: (mandatory) sparse count matrix; raw count data is expected with genes in rows, cells in columns
tpm_matrix: sparse count matrix; TPM like count data is expected with genes in rows, cells in columns
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 (default = 0)
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", 300))
)

ds <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset")