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. "propeller" uses the optional speckle backend for pairwise empirical Bayes moderated tests; see RunPropeller for transformations and parameters.

Usage

RunProportionTest(
  object,
  group.by,
  split.by = NULL,
  comparison = NULL,
  proportion_method,
  sample.by = NULL,
  pseudo_sample_n = 3L,
  allow_pseudo_samples = FALSE,
  n_permutations = 1000,
  FDR_threshold = 0.05,
  log2FD_threshold = log2(1.5),
  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.
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. Required for "milo", "sccoda", and "propeller" unless allow_pseudo_samples = TRUE. For Milo and Propeller, sample IDs may recur across two conditions for a fully paired design; partially paired comparisons are rejected.
pseudo_sample_n: Number of virtual samples per split.by group when a sample-level method has no usable sample.by and allow_pseudo_samples = TRUE. Virtual samples are descriptive only; inferential statistics are set to NA.
allow_pseudo_samples: Explicitly allow descriptive virtual samples when biological sample IDs are unavailable. The default is FALSE because partitioning cells does not create biological replicates.
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, 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.
...: Arguments passed to other functions.

References

Miller SA, Policastro RA, Sriramkumar S, et al. (2021). LSD1 and Aberrant DNA Methylation Mediate Persistence of Enteroendocrine Progenitors That Support BRAF-Mutant Colorectal Cancer. Cancer Research, 81(14), 3791-3805. doi:10.1158/0008-5472.CAN-20-3562

scProportionTest, miloR, scCODA, propeller/speckle

Examples

data(pancreas_sub)
pancreas_sub <- RunProportionTest(
  pancreas_sub,
  group.by = "CellType",
  split.by = "Phase",
  proportion_method = "permutation",
  comparison = list(c("G2M", "G1"))
)
#> ℹ [2026-11-12 06:00:06] Start proportion test ("permutation")
#> ℹ [2026-11-12 06:00:06] Running comparison: "G2M" vs "G1"
#> ℹ [2026-11-12 06:00:07] Running comparison: "G1" vs "G2M"
#> ✔ [2026-11-12 06:00:07] Proportion test completed ("permutation")

ProportionTestPlot(
  pancreas_sub
)

Usage

Arguments

References

See also

Examples