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Pipeline step: Harmony v2 batch correction

step_harmony_v2_sc.Rd

Wraps harmony_v2_sc() as an ScStep.

Usage

step_harmony_v2_sc(
  batch_column,
  additional_batch_columns = NULL,
  modality = c("rna", "adt"),
  harmony_params = params_sc_harmony_v2(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

batch_column

String. Column name in the object containing the primary batch labels.

additional_batch_columns

Optional character vector. Additional batch columns to regress out. If NULL, only the primary batch column is used.

modality

String. One of c("rna", "adt"). You can only use "adt" on SingleCellsMultiModal class.

harmony_params

List. Output of params_sc_harmony_v2().

seed

Integer. For reproducibility.

.verbose

Boolean or integer. Controls verbosity and returns run times. FALSE -> quiet, TRUE or 1L -> normal verbosity, 2L -> detailed verbosity.

Value

An ScStep.

Examples

# the v2 implementation writes its own embedding name
step_harmony_v2_sc(batch_column = "batch_index") %>>%
  step_neighbours_sc(embd_to_use = "harmony_v2")
#> <ScPipeline> 2 steps
#>   1. harmony_v2  batch_column = "batch_index", additional_batch_columns = NULL, modality = c("rna", "adt"), harmony_params = <params_sc_harmony_v2>, seed = 42L, .verbose = TRUE
#>   2. neighbours  embd_to_use = "harmony_v2", no_embd_to_use = NULL, modality = c("rna", "adt"), neighbours_params = <list>, seed = 42L, .verbose = TRUE