PrepareBridgeReference | R Documentation |
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
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
)
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 |
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:
|
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) |
Returns a BridgeReferenceSet
that can be used as input to
FindBridgeTransferAnchors
.
The parameters used are stored in the BridgeReferenceSet
as well
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