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