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Run fastMNN

integration_fastmnn.Rd

Run fastMNN

Usage

integration_fastmnn(
  sobj,
  split_by,
  assay = NULL,
  features = 2000,
  reduction.name = "mnn",
  reduction.key = "mnn_",
  reconstructed.assay = "mnn.reconstructed",
  verbose = TRUE,
  ...
)

Arguments

sobj

: a Seurat object

split_by

CHARACTER : column in sobj@meta.data correspond to batch information (no default)

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