Processing the reference single-cell data

Processing the reference single-cell data

Usage

setup.ref(
  ref_data,
  ref_annotations = NULL,
  ref_subcluster_size = 10,
  max_genes = 5000,
  remove_mt = TRUE,
  verbose = FALSE
)

Arguments

ref_data

A gene x cell matrix of gene expressions. Can be a matrix-like object or a Seurat/AnnData object.

ref_annotations

A character vector (one for each cell) or a single vector pointing to the slot in the Seurat/AnnData object

ref_subcluster_size

An integer. Maximum number of sub-clusters per sub-population.

max_genes

An integer. Maximum number of genes to pick.

remove_mt

Boolean. Whether mitochondrial genes must be removed.

verbose

Boolean. Whether progress should be displayed.

Value

A list containing the processed ref data.

Examples

data(dot.sample)
dot.ref <- setup.ref(dot.sample$ref$counts[, 1:1000], dot.sample$ref$labels[1:1000], 2)