RareQ rare-cell population detection

Usage

RunRareQ(
  srt,
  assay = NULL,
  reduction = "pca",
  dims = 1:30,
  k.param = 20,
  k = 6,
  Q_cut = 0.6,
  ratio = 0.2,
  max_iter = 100,
  run_neighbors = TRUE,
  force_recalc = FALSE,
  neighbor_name = NULL,
  find_neighbors_params = list(),
  rare_threshold = 0.01,
  prefix = "RareQ",
  cluster_colname = paste0(prefix, "_cluster"),
  q_colname = paste0(prefix, "_Q"),
  size_colname = paste0(prefix, "_cluster_size"),
  rare_colname = paste0(prefix, "_is_rare"),
  tool_name = "RareQ",
  verbose = TRUE
)

Arguments

srt: A Seurat object.
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.
reduction: Reduction used to build nearest neighbors when the required {assay}.nn neighbor slot is absent or force_recalc = TRUE. If NULL, DefaultReduction() is used.
dims: Dimensions from reduction used for nearest-neighbor search.
k.param: Number of nearest neighbors to compute with Seurat::FindNeighbors() when neighbor search is needed.
k: Number of nearest neighbors used by RareQ to compute Q values.
Q_cut: Q-value threshold passed to RareQ::FindRare().
ratio: Merge-ratio threshold passed to RareQ::FindRare().
max_iter: Maximum number of RareQ propagation iterations.
run_neighbors: Whether to build the required Seurat neighbor slot if it is missing.
force_recalc: Whether to rebuild the Seurat neighbor slot before running RareQ.
neighbor_name: Name of the Seurat Neighbor object to reuse or create. If NULL, defaults to {assay}.nn, which is the neighbor slot required by RareQ::ComputeQ() and RareQ::FindRare(). A non-default neighbor is copied to {assay}.nn before running RareQ because RareQ reads that slot directly.
find_neighbors_params: Additional named parameters passed to Seurat::FindNeighbors() when neighbor search is run.
rare_threshold: Cluster-size threshold used to mark rare clusters. A value smaller than 1 is treated as a fraction of cells; a value of 1 or larger is treated as a cell count. Set to NULL to skip rare flags.
prefix: Prefix used for metadata columns.
cluster_colname, q_colname, size_colname, rare_colname: Metadata column names for RareQ clusters, Q values, cluster sizes, and rare-cluster flags.
tool_name: Name of the srt@tools entry.
verbose: Whether to print the message. Default is TRUE.

Value

A Seurat object with RareQ results in metadata and srt@tools[[tool_name]].

References

Fa, B. et al. Cell neighborhood topology directs rare cell population identification. Nature Communications (2026). doi:10.1038/s41467-026-71180-x

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(
  pancreas_sub,
  verbose = FALSE
)
pancreas_sub <- RunRareQ(
  pancreas_sub,
  dims = 1:20
)

CellDimPlot(
  pancreas_sub,
  group.by = "RareQ_cluster"
)

CellDimPlot(
  pancreas_sub,
  group.by = "RareQ_is_rare"
)

FeatureDimPlot(
  pancreas_sub,
  features = "RareQ_Q"
)