Permutation-based proportion test

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 (log2(group1 / group2)).

Usage

RunPermutation(
  object,
  group.by,
  split.by,
  comparison = NULL,
  n_permutations = 1000,
  include_all_cells = FALSE,
  seed = 11,
  verbose = TRUE,
  srt = NULL
)

Arguments

object

A Seurat object.

group.by

Metadata column(s) used to color cells.

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; a separate biological sample column is still required unless descriptive virtual samples are explicitly enabled.

comparison

Optional pairs of condition labels. Each pair is c(group1, group2). obs_log2FD is log2(group1 / group2), matching RunDEtest / Seurat ident.1 vs ident.2: positive values mean the cell type is more abundant in group1. If NULL, all pairwise comparisons are generated in both directions.

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.

seed

Random seed, including for permutation testing.

verbose

Whether to print the message. Default is TRUE.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A method result bundle used internally by RunProportionTest.