calculate_delta_variance: Calculate delta variance

In neurorestore/Libra: Differential expression utilizing biological replicates in single-cell data

Calculate delta variance

Description

Calculate delta variance from a single-cell matrix.

Usage

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

Arguments

input	a single-cell matrix to be converted, with features (genes) in rows and cells in columns. Alternatively, a Seurat, monocle3, or or SingleCellExperiment object can be directly input.
meta	the accompanying meta data whereby the rownames match the column names of input. If a Seurat, monocle3 or SingleCellExperiment object is provided this can be null.
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 replicates expressing a gene to retain it. Defaults to 0

Value

a list of pseudobulk matrices, for each cell type.

neurorestore/Libra documentation built on Aug. 31, 2024, 8:53 p.m.