RunFastMNN: Run fastMNN

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

Run fastMNN

Description

Run fastMNN

Usage

RunFastMNN(
  object.list,
  assay = NULL,
  features = 2000,
  reduction.name = "mnn",
  reduction.key = "mnn_",
  reconstructed.assay = "mnn.reconstructed",
  verbose = TRUE,
  ...
)

Arguments

object.list	A list of Seurat objects
assay	Assay to use, defaults to the default assay of the first object
features	Either a list of features to use when calculating batch correction, or a number (2000 by default) of variable features to select.
reduction.name	Name to store resulting DimReduc object as
reduction.key	Key for resulting DimReduc
reconstructed.assay	Name for the assay containing the low-rank reconstruction of the expression matrix.
verbose	Print messages from SelectIntegrationFeatures
...	Extra parameters passed to fastMNN

Value

A Seurat object merged from the objects in object.list and a new DimReduc of name reduction.name (key set to reduction.key) with corrected embeddings matrix as well as the rotation matrix used for the PCA stored in the feature loadings slot. Also returns an expression matrix reconstructed from the low-rank approximation in the reconstructed.assay assay; all other metadata info fastMNN is stored in the tool slot, accessible with Tool

See Also

fastMNN Tool

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.