Bulk reference — splat_bulk_reference • viewmastR

This function creates a seurat object (typically single cell genomics) of multiple single cell profiles from each sample from a bulk object (SummarizedExperiment or Seurat object currently supported). In doing so, the function creates single cell profiles with a size distribution that approximates the provided single cell object (query)

Usage

splat_bulk_reference(
  query = NULL,
  ref,
  N = 2,
  assay = "RNA",
  bulk_feature_row = "gene_short_name",
  bulk_assay_name = "RNA",
  dist = c("sc-direct", "sc-mimic", "bulk"),
  seed = 42
)

Arguments

query: a single cell object (Seurat) with a size distribution of counts to be mimicked in the assay argument
ref: the reference object (SummarizedExperiment or Seurat)
N: the number of simulated cells to create per bulk sample
assay: the assay slot of the query (Seurat)
bulk_feature_row: the column name of gene symbols in ref (only used if ref is SummarizedExperiment)
bulk_assay_name: the name of the assay object in the ref
dist: distribution method: "sc-direct", "sc-mimic", or "bulk"
seed: random seed for reproducibility

Value

a classified seurat object labeled according to the bulk reference