RunProportionTest performs differential abundance testing for cell proportions through a unified dispatcher.
Usage
RunProportionTest(
srt,
group.by,
split.by,
comparison = NULL,
proportion_method,
sample.by = NULL,
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 a metadata column for cell type/group labels.
- split.by
Name of a metadata column defining conditions to compare.
- comparison
Optional comparisons to perform. Supports
list(c("A", "B"))or character values like"A_vs_B".- proportion_method
Differential abundance method. Canonical values are
"permutation","milo","sccoda", and"propeller". Alias values (for example"permutation_test"or"perm") are accepted and normalized to"permutation".- sample.by
Metadata column for biological sample IDs. Required for
"milo","sccoda", and"propeller".- n_permutations
Number of permutations for permutation mode.
- 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 permutation complete grid.
- seed
Random seed.
- verbose
Whether to print messages.
- ...
Additional arguments passed to the selected method function.
Examples
data(pancreas_sub)
pancreas_sub <- RunProportionTest(
pancreas_sub,
group.by = "CellType",
split.by = "Phase",
proportion_method = "permutation",
comparison = list(c("G2M", "G1"))
)
#> ℹ [2026-04-26 02:25:03] Start proportion test ("permutation")
#> ℹ [2026-04-26 02:25:03] Running comparison: "G1" vs "G2M"
#> ℹ [2026-04-26 02:25:10] Running comparison: "G2M" vs "G1"
#> ✔ [2026-04-26 02:25:17] Proportion test completed ("permutation")
ProportionTestPlot(pancreas_sub)
