FindBridgeTransferAnchors: Find bridge anchors between query and extended...
In satijalab/seurat: Tools for Single Cell Genomics

FindBridgeTransferAnchors

R Documentation

Find bridge anchors between query and extended bridge-reference

Description

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.

Usage

FindBridgeTransferAnchors(
  extended.reference,
  query,
  query.assay = NULL,
  dims = 1:30,
  scale = FALSE,
  reduction = c("lsiproject", "pcaproject"),
  bridge.reduction = c("direct", "cca"),
  verbose = TRUE
)

Arguments

`extended.reference`	BridgeReferenceSet object generated from `PrepareBridgeReference`
`query`	A query Seurat object
`query.assay`	Assay name for query-bridge integration
`dims`	Number of dimensions for query-bridge integration
`scale`	Determine if scale the query data for projection
`reduction`	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.
`bridge.reduction`	Dimensional reduction to perform when finding anchors. Can be one of: cca: Canonical correlation analysis direct: Use assay data as a dimensional reduction
`verbose`	Print messages and progress