View source: R/harmony_option.R
harmony_options | R Documentation |
Set advanced parameters for RunHarmony
harmony_options(
alpha = 0.2,
tau = 0,
block.size = 0.05,
max.iter.cluster = 20,
epsilon.cluster = 0.001,
epsilon.harmony = 0.01
)
alpha |
When setting lambda = NULL and use lambda estimation mode, lambda would be determined by the expected number of cells assuming idependece between batches and clusters. i.e., lambda = alpha * expected number of cells, default 0.2 and alpha should be 0 < alpha < 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. |
Return a list for '.options' argument of 'RunHarmony'
## If want to set max.iter.cluster to be 100, do
## Not run:
RunHarmony(data_meta, meta_data, vars_use,
.options = harmony_options(max.iter.cluster = 100))
## End(Not run)
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