Propeller differential abundance wrapper

Method-specific implementation used by RunProportionTest when proportion_method = "propeller". Uses the optional speckle backend: getTransformedProps() computes the transformed proportions and propeller.ttest() performs limma empirical Bayes moderated tests. Each requested comparison is a two-group test; multiple conditions produce pairwise results, not an omnibus ANOVA. P-values, FDR, and Tstatistic come from speckle. obs_log2FD and bootstrap intervals describe the ratio of mean untransformed sample proportions, with a 1e-5 pseudocount; these intervals are not moderated-test intervals.

Usage

RunPropeller(
  object,
  group.by,
  split.by,
  sample.by,
  comparison = NULL,
  n_bootstrap = 1000,
  seed = 11,
  verbose = TRUE,
  srt = NULL,
  transform = c("logit", "asin"),
  robust = TRUE,
  trend = FALSE
)

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.
sample.by: Metadata column identifying biological samples. Required when calling RunPropeller() directly. Fully paired sample IDs across two conditions add a sample blocking effect to the speckle design matrix; partially paired comparisons are rejected. At least two biological samples per condition are required.
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 sample bootstrap iterations for descriptive confidence intervals. Paired samples are resampled together. Use zero to omit bootstrap intervals.
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.
transform: Proportion transformation, "logit" (default) or "asin". Logit uses speckle's count pseudocount of 0.5 before computing proportions.
robust: Whether speckle uses robust empirical Bayes variance shrinkage.
trend: Whether speckle fits a mean-variance trend.

Value

A method result bundle used internally by RunProportionTest.