FindBridgeIntegrationAnchors: Find integration 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. These integration anchors can later be used to integrate query and reference using the IntegrateEmbeddings object.

Usage

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

Value

Returns an AnchorSet object that can be used as input to IntegrateEmbeddings.

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.

integration.reduction

Dimensional reduction to perform when finding anchors between query and reference. Options are:

direct: find anchors directly on the bridge representation space
cca: perform cca on the on the bridge representation space and then find anchors

verbose

Print messages and progress