harmony (version 1.0.1)

harmony_options: Set advanced options for RunHarmony

Description

Set advanced options for RunHarmony

Usage

harmony_options(
  lambda_range = c(0.1, 10),
  tau = 0,
  block.size = 0.05,
  max.iter.cluster = 20,
  epsilon.cluster = 1e-05,
  epsilon.harmony = 1e-04
)

Value

Return a list for `.options` argument of `RunHarmony`

Arguments

lambda_range

Default lambda_range = c(0.1, 10). Lambda is ridge regression penalty parameter and smaller values result in more aggressive correction. During harmony iterations, the appropriate value of lambda is dynamically estimated. And parameter `lambda_range` set the allowed range for lambda estimation. e.g. `lambda_range` = c(0.1, 10) means that lambda can only vary between 0.1 and 10 when being dynamically estimated. Note that when setting the upper and lower bound of lambda_range to the same value would result in using a fixed lambda throughout harmony iterations. e.g. `lambda_range` = c(1,1) would make harmony using a fixed lambda = 1.

tau

Protection against overclustering small datasets with large ones. `tau` is the expected number of cells per cluster.

block.size

What proportion of cells to update during clustering. Between 0 to 1, default 0.05. Larger values may be faster but less accurate.

max.iter.cluster

Maximum number of rounds to run clustering at each round of Harmony.

epsilon.cluster

Convergence tolerance for clustering round of Harmony. Set to -Inf to never stop early.

epsilon.harmony

Convergence tolerance for Harmony. Set to -Inf to never stop early. When `epsilon.harmony` is set to not NULL, then user-supplied values of `early_stop` is ignored.

Examples

## If want to set lambda to be fixed to 1, do
if (FALSE) {
RunHarmony(data_meta, meta_data, vars_use,
              .options = harmony_options(lambda = c(1, 1)))
}