Estimate useful dimensions from a reduction

Usage

RunDimsEstimate(
  srt,
  reduction = NULL,
  reduction_method = NULL,
  k = 20L,
  min_dims = 20L,
  fallback_max_dims = 50L,
  skip_first = FALSE,
  use_stored = TRUE,
  verbose = TRUE
)

Arguments

srt: A Seurat object.
reduction: Name of the dimensional reduction to inspect. Default is NULL, which automatically selects a PCA-like reduction via DefaultReduction() with pattern = "pca".
reduction_method: Optional reduction method name. When set to "nmf" or "glmpca", all available dimensions will be retained.
k: Number of neighbors used by intrinsicDimension::maxLikGlobalDimEst. Default is 20.
min_dims: Minimum number of dimensions kept when intrinsic-dimension estimation succeeds. Default is 20.
fallback_max_dims: Maximum number of dimensions kept when no valid estimate is available. Default is 50.
skip_first: Whether to drop the first dimension from the returned result. Useful for TFIDF/LSI workflows. Default is FALSE.
use_stored: Whether to use misc$dims_estimate already stored in the reduction when available. Default is TRUE.
verbose: Whether to print the message. Default is TRUE.

Value

An integer vector of dimensions to use.