Permutation-based proportion test — RunPermutation • scop

Method-specific implementation used by RunProportionTest when proportion_method = "permutation". This method is a permutation-based statistical test for compositional shift rather than a dedicated biological model. Bootstrap confidence intervals are reported as uncertainty estimates for observed log2 fold-differences.

Usage

RunPermutation(
  srt,
  group.by,
  split.by,
  comparison = NULL,
  n_permutations = 1000,
  include_all_cells = FALSE,
  verbose = TRUE
)

Arguments

srt: A Seurat object.
group.by: Name of one or more meta.data columns to group (color) cells by.
split.by: Metadata column that identifies the condition groups to compare. For sample-level methods, if split.by is omitted and sample.by is provided, sample.by is treated as the condition column and virtual samples are created within each condition.
comparison: Optional: specify comparisons to perform.
n_permutations: Number of permutations for permutation-based test.
include_all_cells: Whether to include all cell types in the complete grid for permutation mode.
verbose: Whether to print the message. Default is TRUE.

Value

A method result bundle used internally by RunProportionTest.