PrepareBridgeReference: Prepare the bridge and reference datasets

In Seurat: Tools for Single Cell Genomics

Prepare the bridge and reference datasets

Description

Preprocess the multi-omic bridge and unimodal reference datasets into an extended reference. This function performs the following three steps: 1. Performs within-modality harmonization between bridge and reference 2. Performs dimensional reduction on the SNN graph of bridge datasets via Laplacian Eigendecomposition 3. Constructs a bridge dictionary representation for unimodal reference cells

Usage

PrepareBridgeReference(
  reference,
  bridge,
  reference.reduction = "pca",
  reference.dims = 1:50,
  normalization.method = c("SCT", "LogNormalize"),
  reference.assay = NULL,
  bridge.ref.assay = "RNA",
  bridge.query.assay = "ATAC",
  supervised.reduction = c("slsi", "spca", NULL),
  bridge.query.reduction = NULL,
  bridge.query.features = NULL,
  laplacian.reduction.name = "lap",
  laplacian.reduction.key = "lap_",
  laplacian.reduction.dims = 1:50,
  verbose = TRUE
)

Arguments

reference	A reference Seurat object
bridge	A multi-omic bridge Seurat object
reference.reduction	Name of dimensional reduction of the reference object (default is 'pca')
reference.dims	Number of dimensions used for the reference.reduction (default is 50)
normalization.method	Name of normalization method used: LogNormalize or SCT
reference.assay	Assay name for reference (default is DefaultAssay)
bridge.ref.assay	Assay name for bridge used for reference mapping. RNA by default
bridge.query.assay	Assay name for bridge used for query mapping. ATAC by default
supervised.reduction	Type of supervised dimensional reduction to be performed for integrating the bridge and query. Options are: slsi: Perform supervised LSI as the dimensional reduction for the bridge-query integration spca: Perform supervised PCA as the dimensional reduction for the bridge-query integration NULL: no supervised dimensional reduction will be calculated. bridge.query.reduction is used for the bridge-query integration
bridge.query.reduction	Name of dimensions used for the bridge-query harmonization. 'bridge.query.reduction' and 'supervised.reduction' cannot be NULL together.
bridge.query.features	Features used for bridge query dimensional reduction (default is NULL which uses VariableFeatures from the bridge object)
laplacian.reduction.name	Name of dimensional reduction name of graph laplacian eigenspace (default is 'lap')
laplacian.reduction.key	Dimensional reduction key (default is 'lap_')
laplacian.reduction.dims	Number of dimensions used for graph laplacian eigenspace (default is 50)
verbose	Print progress and message (default is TRUE)

Value

Returns a BridgeReferenceSet that can be used as input to FindBridgeTransferAnchors. The parameters used are stored in the BridgeReferenceSet as well

Seurat documentation built on June 8, 2025, 12:24 p.m.