Proportion Test

RunProportionTest performs differential abundance testing for cell proportions. The function acts as a dispatcher and routes to one of the method-specific implementations: permutation, milo, sccoda, or propeller.

Usage

RunProportionTest(
  srt,
  group.by,
  split.by = NULL,
  comparison = NULL,
  proportion_method,
  sample.by = NULL,
  pseudo_sample_n = 3L,
  n_permutations = 1000,
  FDR_threshold = 0.05,
  log2FD_threshold = log2(1.5),
  include_all_cells = FALSE,
  seed = 11,
  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.

proportion_method

Differential abundance method. One of "permutation", "milo", "sccoda", or "propeller". This argument is required. Alias values such as "permutation_test" and "perm" are accepted and normalized to "permutation".

sample.by

Metadata column that identifies biological samples. For "milo", "sccoda", and "propeller", when sample.by is omitted or identical to split.by, virtual samples are created within each split.by group for convenience.

pseudo_sample_n

Number of virtual samples per split.by group when a sample-level method has no usable sample.by.

n_permutations

Number of permutations for permutation-based test.

FDR_threshold

FDR value cutoff for significance.

log2FD_threshold

Absolute value of log2FD cutoff for significance.

include_all_cells

Whether to include all cell types in the complete grid for permutation mode.

seed

Random seed.

verbose

Whether to print the message. Default is TRUE.

...

Additional arguments passed to the selected method function.

References

Miller et al. paper, scProportionTest, miloR, scCODA, propeller/speckle

See also

RunPermutation, RunMilo, RunscCODA, RunPropeller, ProportionTestPlot

Examples

data(pancreas_sub)
pancreas_sub <- RunProportionTest(
  pancreas_sub,
  group.by = "CellType",
  split.by = "Phase",
  proportion_method = "permutation",
  comparison = list(c("G2M", "G1"))
)
#> ℹ [2026-05-14 07:35:36] Start proportion test ("permutation")
#> ℹ [2026-05-14 07:35:36] Running comparison: "G1" vs "G2M"
#> ℹ [2026-05-14 07:35:36] Running comparison: "G2M" vs "G1"
#> ✔ [2026-05-14 07:35:36] Proportion test completed ("permutation")

ProportionTestPlot(
  pancreas_sub
)