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Proportion Test

Source: R/RunProportionTest.R
RunProportionTest.Rd

RunProportionTest performs a Monte-carlo permutation test to quantify the cell proportion differences between each condition.

Usage

RunProportionTest(
  srt,
  group.by,
  split.by,
  comparison = NULL,
  n_permutations = 1000,
  FDR_threshold = 0.05,
  log2FD_threshold = log2(1.5),
  include_all_cells = FALSE,
  verbose = TRUE
)

Arguments

srt

A Seurat object.

group.by

Name of one or more meta.data columns to group (color) cells by.

split.by

Name of a column in meta.data column to split plot by. Default is NULL.

comparison

Optional: specify comparisons to perform.

n_permutations

Number of permutations for the 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 (default: FALSE).

verbose

Whether to print the message. Default is TRUE.

References

Miller et al. paper, scProportionTest

See also

ProportionTestPlot

Examples

data(pancreas_sub)
# Default behavior: only include cell types present in comparison groups
pancreas_sub <- RunProportionTest(
  pancreas_sub,
  group.by = "CellType",
  split.by = "Phase",
  comparison = list(c("G2M", "G1"))
)
#> ℹ [2026-01-27 08:23:05] Start proportion test
#> ℹ [2026-01-27 08:23:05] Running comparison: "G1" vs "G2M"
#> ℹ [2026-01-27 08:23:12] Running comparison: "G2M" vs "G1"
#> ✔ [2026-01-27 08:23:19] Proportion test completed

# Include all cell types from the dataset
pancreas_sub <- RunProportionTest(
  pancreas_sub,
  group.by = "CellType",
  split.by = "Phase",
  comparison = list(c("G2M", "G1")),
  include_all_cells = TRUE
)
#> ℹ [2026-01-27 08:23:19] Start proportion test
#> ℹ [2026-01-27 08:23:19] Running comparison: "G1" vs "G2M"
#> ℹ [2026-01-27 08:23:27] Running comparison: "G2M" vs "G1"
#> ✔ [2026-01-27 08:23:34] Proportion test completed

ProportionTestPlot(
  pancreas_sub
)