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Run Harmony v2 (GPU)

harmony_v2_gpu_sc.Rd

A GPU-accelerated version of Harmony v2 by Patikas et al., 2026, implemented in Rust. Performs batch correction on PCA embeddings and stores the result as a "harmony_gpu" embedding in the object. Only a single batch covariate is supported on the GPU path.

Usage

harmony_v2_gpu_sc(
  object,
  batch_column,
  modality = c("rna", "adt"),
  harmony_params = params_sc_harmony_v2_gpu(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

batch_column

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

modality

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

harmony_params

List. Output of params_sc_harmony_v2_gpu().

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

The object with a "harmony_gpu" embedding added. If no PCA embeddings are found, returns the object unchanged with a warning.