rliger: optimizeNewLambda – R documentation

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optimizeNewLambda

Perform factorization for new lambda value

Description

Uses an efficient strategy for updating that takes advantage of the information in the existing factorization; uses previous k. Recommended mainly when re-optimizing for higher lambda and when new lambda value is significantly different; otherwise may not return optimal results.

Usage

optimizeNewLambda(
  object,
  new.lambda,
  thresh = 1e-04,
  max.iters = 100,
  rand.seed = 1,
  verbose = TRUE
)

Arguments

`object`	`liger` object. Should call optimizeALS before calling.
`new.lambda`	Regularization parameter. Larger values penalize dataset-specific effects more strongly.
`thresh`	Convergence threshold. Convergence occurs when \|obj0-obj\|/(mean(obj0,obj)) < thresh
`max.iters`	Maximum number of block coordinate descent iterations to perform (default 100).
`rand.seed`	Random seed for reproducibility (default 1).
`verbose`	Print progress bar/messages (TRUE by default)

Value

liger object with optimized factorization values

Examples

## Not run: 
# decide to run with lambda = 15 instead (keeping k the same)
ligerex <- optimizeNewLambda(ligerex, new.lambda = 15)

## End(Not run)

rliger

Linked Inference of Genomic Experimental Relationships

v1.0.0

GPL-3

Authors

Joshua Welch [aut, ctb], Chao Gao [aut, ctb, cre], Jialin Liu [aut, ctb], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb]

Initial release

2021-04-18