PrepareBridgeReference: 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
)

Value

Returns a BridgeReferenceSet that can be used as input to

FindBridgeTransferAnchors. The parameters used are stored in the BridgeReferenceSet as well

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)