Create a pseudobulk matrix

Convert a single-cell expression matrix (i.e., genes by cells) to a pseudobulk matrix by summarizing counts within biological replicates. This function is

Usage

to_pseudobulk(
  input,
  meta = NULL,
  replicate_col = "replicate",
  cell_type_col = "cell_type",
  label_col = "label",
  min_cells = 3,
  min_reps = 2,
  min_features = 0,
  external = T
)

Arguments

input

a single-cell matrix to be converted, with features (genes) in rows and cells in columns. Alternatively, a Seurat, monocole3, or or SingleCellExperiment object can be directly input.

meta

the accompanying meta data whereby the rownames match the column names of input.

replicate_col

the vector in meta containing the replicate information. Defaults to replicate.

cell_type_col

the vector in meta containing the cell type information. Defaults to cell_type.

label_col

the vector in meta containing the experimental label. Defaults to label.

min_cells

the minimum number of cells in a cell type to retain it. Defaults to 3.

min_reps

the minimum number of replicates in a cell type to retain it. Defaults to 2.

min_features

the minimum number of expressing cells (or replicates) for a gene to retain it. Defaults to 0.

Value

a list of pseudobulk matrices, for each cell type.