Canonical signature testing interface

Usage

test_signature(
  score,
  group = NULL,
  sample = NULL,
  celltype = NULL,
  target_celltype = NULL,
  region = NULL,
  pseudotime = NULL,
  lineage = NULL,
  level = c("cell", "sample", "celltype", "sample_celltype", "pseudobulk", "region",
    "sample_region", "trajectory"),
  method = c("wilcox", "t", "lm", "limma", "edgeR", "DESeq2", "spearman", "tradeSeq"),
  ref_group = NULL,
  paired = FALSE,
  covariates = NULL,
  adjust_method = "BH",
  min_cells = 10,
  min_samples = 2,
  aggregation = c("mean", "median", "fraction", "sum"),
  threshold = 0,
  backend = c("auto", "internal", "monocle3", "monocle", "slingshot"),
  verbose = TRUE
)

Arguments

score: gleam_score object.
group: Group variable (column name or vector).
sample: Sample variable (column name or vector).
celltype: Celltype variable (column name or vector).
target_celltype: Target celltype label for within-celltype group comparisons.
region: Spatial region/domain variable (column name or vector).
pseudotime: Pseudotime source for trajectory mode.
lineage: Lineage source for trajectory mode.
level: Comparison level.
method: Statistical method.
ref_group: Reference group.
paired: Placeholder, currently ignored.
covariates: Placeholder, currently ignored.
adjust_method: Multiple testing adjustment method.
min_cells: Minimum cells per group.
min_samples: Minimum samples per group.
aggregation: Aggregation summary used by pseudobulk levels.
threshold: Threshold used when aggregation = 'fraction'.
backend: Trajectory backend used when level = 'trajectory'.
verbose: Print messages.

Value

An object of class gleam_test.