RunOptimizeALS: Run optimizeALS on a Seurat object

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

Run optimizeALS on a Seurat object

Description

Run optimizeALS on a Seurat object

Usage

RunOptimizeALS(
  object,
  k,
  assay = NULL,
  split.by = "orig.ident",
  lambda = 5,
  thresh = 1e-06,
  max.iters = 30,
  reduction.name = "iNMF_raw",
  reduction.key = "riNMF_",
  nrep = 1,
  H.init = NULL,
  W.init = NULL,
  V.init = NULL,
  rand.seed = 1,
  print.obj = FALSE,
  ...
)

Arguments

object	A merged Seurat object
k	Inner dimension of factorization (number of factors). Run suggestK to determine appropriate value; a general rule of thumb is that a higher k will be needed for datasets with more sub-structure.
assay	Assay to use, defaults to the default assay of the first object
split.by	Attribute for splitting, defaults to "orig.ident"
lambda	Regularization parameter. Larger values penalize dataset-specific effects more strongly (ie. alignment should increase as lambda increases). Run suggestLambda to determine most appropriate value for balancing dataset alignment and agreement (default 5.0).
thresh	Convergence threshold. Convergence occurs when |obj0-obj|/(mean(obj0,obj)) < thresh. (default 1e-6)
max.iters	Maximum number of block coordinate descent iterations to perform (default 30).
reduction.name	Name to store resulting DimReduc object as
reduction.key	Key for resulting DimReduc
nrep	Number of restarts to perform (iNMF objective function is non-convex, so taking the best objective from multiple successive initializations is recommended). For easier reproducibility, this increments the random seed by 1 for each consecutive restart, so future factorizations of the same dataset can be run with one rep if necessary. (default 1)
H.init	Initial values to use for H matrices. (default NULL)
W.init	Initial values to use for W matrix (default NULL)
V.init	Initial values to use for V matrices (default NULL)
rand.seed	Random seed to allow reproducible results (default 1).
print.obj	Print objective function values after convergence (default FALSE).
...	Arguments passed to other methods

Value

A Seurat object with embeddings and loadings from optimizeALS stored as a DimReduc object with name reduction.name (key set to reduction.key); per-dataset feature loadings matrices stored in the tool slot, accessible with Tool

See Also

optimizeALS Tool

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.