Obtain the range of values to downsample at (either for individuals, or mean number of cells per individual), for bulk analysis

Obtain the range of values to downsample at (either for individuals, or mean number of cells per individual), for bulk analysis

bulk_downsampling_range(
  SCEs,
  celltype_correspondence,
  sampled = "individuals",
  sampleIDs = "donor_id",
  celltypeIDs = "cell_type"
)

Arguments

SCEs

A list of SingleCellExperiment (SCE) objects, each representing a scRNA-seq dataset.

celltype_correspondence

A named vector that maps a standard cell type label (e.g., "Endo", "Micro") to how that cell type appears in each dataset. Use NA if the cell type is not present in a given dataset.

sampled

Specifies the unit of down-sampling. Can be either "individuals" or "cells", depending on whether the analysis downsamples across samples or cells.

sampleIDs

A character vector specifying the column name in each SCE that represents sample or donor IDs (in order of SCEs).

celltypeIDs

A character vector specifying the column name in each SCE that denotes cell type identity (in order of SCEs).

Value

list containing values which the data will be downsampled at, in ascending order