Permutation-based proportion test

Method-specific permutation implementation used by RunProportionTest. This is a permutation-based statistical test for compositional shift (not a separate biological model). Bootstrap confidence intervals are included as uncertainty estimates for observed log2 fold-differences.

Usage

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

Arguments

srt

A Seurat object.

group.by

Cell-type metadata column.

split.by

Condition metadata column.

comparison

Optional comparisons to perform.

n_permutations

Number of permutations.

include_all_cells

Whether to include all cell types in grid completion.

verbose

Whether to print messages.

See also

RunProportionTest