Find a set of anchors between unimodal query and the other unimodal reference
using a pre-computed BridgeReferenceSet.
This function performs three steps:
1. Harmonize the bridge and query cells in the bridge query reduction space
2. Construct the bridge dictionary representations for query cells
3. Find a set of anchors between query and reference in the bridge graph laplacian eigenspace
These anchors can later be used to integrate embeddings or transfer data from the reference to
query object using the MapQuery object.
FindBridgeTransferAnchors(
extended.reference,
query,
query.assay = NULL,
dims = 1:30,
scale = FALSE,
reduction = c("lsiproject", "pcaproject"),
bridge.reduction = c("direct", "cca"),
verbose = TRUE
)Returns an AnchorSet object that can be used as input to
TransferData, IntegrateEmbeddings and
MapQuery.
BridgeReferenceSet object generated from
PrepareBridgeReference
A query Seurat object
Assay name for query-bridge integration
Number of dimensions for query-bridge integration
Determine if scale the query data for projection
Dimensional reduction to perform when finding anchors. Options are:
pcaproject: Project the PCA from the bridge onto the query. We recommend using PCA when bridge and query datasets are from scRNA-seq
lsiproject: Project the LSI from the bridge onto the query. We recommend using LSI when bridge and query datasets are from scATAC-seq or scCUT&TAG data. This requires that LSI or supervised LSI has been computed for the bridge dataset, and the same features (eg, peaks or genome bins) are present in both the bridge and query.
Dimensional reduction to perform when finding anchors. Can be one of:
cca: Canonical correlation analysis
direct: Use assay data as a dimensional reduction
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