Calculate the number of possible group combinations — countCombinations • permuteDE

Given two groups of replicates, this function calculates the number of unique ways to divide the replicates into two groups while preserving group sizes. The formula is: C = n!/(k!(n-k)!). (see base function choose)

Usage

countCombinations(
  object = NULL,
  metadata = NULL,
  replicate_labels = NULL,
  group_labels = NULL,
  use_cells = NULL,
  n_replicates = NULL,
  n_group1 = NULL
)

Arguments

object: An optional 'Seurat' or 'SingleCellExperiment' object. If NULL, countCombinations will expect either (1) vector input to parameters replicate_label and group_label or (2) numeric input to parameters n_replicates and n_group1.
metadata: An optional dataframe containing relevant metadata columns corresponding to the data provided to parameter object. Default = NULL looks for metadata in object or other provided inputs.
replicate_labels: A string indicating the name of the metadata column containing the biological replicate labels or a character vector containing the biological replicate labels in order.
group_labels: A string indicating the name of the column containing the two comparison group labels or a character vector containing the comparison labels in order.
use_cells: A vector of cell names to subset prior to calculating possible group comibinations. Default = NULL will use all cells.
n_replicates: A numeric value indicating the total number of replicates. Defaults to NULL.
n_group1: A numeric value indicating the number of replicates in one group (doesn't matter which). Defaults to NULL.

Value

Returns a numeric value indicating the number of all possible group combinations.

Details

Users may provide input in three ways:

(1) A vector of replicate labels and a vector of group labels (in order)

(2) The total number of replicates (n) and the number of replicates in one group (k) (doesn't matter which group).

(3) Column names indicating replicate and group metadata columns in a provided 'Seurat' or 'SingleCellExperiment' object or a provided metadata dataframe.