check_inputs: Check inputs

In smorabit/scWGCNA: hdWGCNA

Check inputs

Description

Check inputs prior to running to_pseudobulk

Usage

check_inputs(
  input,
  meta = meta,
  replicate_col = "replicate",
  cell_type_col = "cell_type",
  label_col = "label"
)

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 cleaned up expression matrix and meta data object

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