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Generate combinations

Source: R/getCombinations.R
getCombinations.Rd

For a set of replicates that belong to two groups, this function will generate a set of randomized group combinations.

Usage

getCombinations(
  object = NULL,
  metadata = NULL,
  replicate_labels = NULL,
  group_labels = NULL,
  use_cells = NULL,
  n_replicates = NULL,
  n_group1 = NULL,
  n_combinations = 1000,
  confound_check = NULL,
  progress_message = "",
  random_seed = 1,
  verbose = TRUE
)

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. Alternately, a vector can be provided to generate combinations when shuffling separately within multiple sets. Defaults to NULL.

n_group1

A numeric value indicating the number of replicates in one group (doesn't matter which). Alternately, a vector can be provided to generate combinations when shuffling separately within multiple sets. Defaults to NULL.

n_combinations

A numeric value indicating the number of combinations to generate. Defaults to 1000.

confound_check

An optional dataframe of covariates for which to exclude permutations that are perfectly confounded. Defaults to NULL.

progress_message

A character string indicating additional progress messaging (internal use). Defaults to "".

random_seed

A numeric value indicating the random seed to be used. Defaults to 1.

verbose

A Boolean value indicating whether to use verbose output during the execution of this function. Defaults to TRUE. Can be set to FALSE for a cleaner output.

Value

Returns a matrix where each column contains a combination of index values indicating which replicates to assign to the first group.

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.