RunHarmony: Run harmony algorithm generic function

Description

This is a generic that provides wrappers for Seurat and SingleCellExperiment objects. Also, it allows harmony standalone with a matrix and a metadata dataframe.

Usage

RunHarmony(...)
# S3 method for Seurat
RunHarmony(
  object,
  group.by.vars,
  reduction.use = "pca",
  dims.use = NULL,
  verbose = TRUE,
  reduction.save = "harmony",
  project.dim = TRUE,
  ...
)
# S3 method for SingleCellExperiment
RunHarmony(
  object,
  group.by.vars,
  dims.use = NULL,
  verbose = TRUE,
  reduction.save = "HARMONY",
  ...
)
HarmonyMatrix(...)

Value

Seurat object. Harmony dimensions placed into a new slot in the Seurat object according to the reduction.save. For downstream Seurat analyses, use reduction='harmony'.

SingleCellExperiment object. After running RunHarmony, the corrected cell embeddings can be accessed with reducedDim(object, "Harmony").

Arguments

...: harmony algorithm parameters to be passed on RunHarmony.default
object: SingleCellExperiment with the PCA reducedDim cell embeddings populated
group.by.vars: the name(s) of covariates that harmony will remove its effect on the data.
reduction.use: Name of dimension reduction to use. Default is pca.
dims.use: a vector of indices that allows only selected cell embeddings features to be used.
verbose: enable verbosity
reduction.save: the name of the new slot that is going to be created by harmony. By default, HARMONY.
project.dim: Project dimension reduction loadings. Default TRUE.