FindBridgeIntegrationAnchors: Find integration bridge anchors between query and extended...

In Seurat: Tools for Single Cell Genomics

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
)

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

Value

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

Seurat documentation built on May 29, 2024, 4:20 a.m.