Propeller differential abundance wrapper

Method-specific implementation used by RunProportionTest when proportion_method = "propeller". This implementation works on sample-level proportions using a propeller-style transformed test and stores standardized outputs for plotting.

Usage

RunPropeller(
  srt,
  group.by,
  split.by,
  sample.by,
  comparison = NULL,
  n_bootstrap = 1000,
  seed = 11,
  verbose = TRUE
)

Arguments

srt: 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 and virtual samples are created within each condition.
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.
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.
n_bootstrap: Number of bootstrap iterations for confidence intervals.
seed: Random seed.
verbose: Whether to print the message. Default is TRUE.

Value

A method result bundle used internally by RunProportionTest.