to_pseudobulk: Create a pseudobulk matrix

In smorabit/scWGCNA: hdWGCNA

Create a pseudobulk matrix

Description

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.

smorabit/scWGCNA documentation built on April 4, 2024, 10:32 a.m.