FindBridgeAnchor: Find bridge anchors between two unimodal datasets
In satijalab/seurat: Tools for Single Cell Genomics

FindBridgeAnchor

R Documentation

Find bridge anchors between two unimodal datasets

Description

First, bridge object is used to reconstruct two single-modality profiles and then project those cells into bridage graph laplacian space. Next, find a set of anchors between two single-modality objects. These anchors can later be used to integrate embeddings or transfer data from the reference to query object using the MapQuery object.

Usage

FindBridgeAnchor(
  object.list,
  bridge.object,
  object.reduction,
  bridge.reduction,
  anchor.type = c("Transfer", "Integration"),
  reference = NULL,
  laplacian.reduction = "lap",
  laplacian.dims = 1:50,
  reduction = c("direct", "cca"),
  bridge.assay.name = "Bridge",
  reference.bridge.stored = FALSE,
  k.anchor = 20,
  k.score = 50,
  verbose = TRUE,
  ...
)

Arguments

`object.list`	A list of Seurat objects
`bridge.object`	A multi-omic bridge Seurat which is used as the basis to represent unimodal datasets
`object.reduction`	A list of dimensional reductions from object.list used to be reconstructed by bridge.object
`bridge.reduction`	A list of dimensional reductions from bridge.object used to reconstruct object.reduction
`anchor.type`	The type of anchors. Can be one of: Integration: Generate IntegrationAnchors for integration Transfer: Generate TransferAnchors for transfering data
`reference`	A vector specifying the object/s to be used as a reference during integration or transfer data.
`laplacian.reduction`	Name of bridge graph laplacian dimensional reduction
`laplacian.dims`	Dimensions used for bridge graph laplacian dimensional reduction
`reduction`	Dimensional reduction to perform when finding anchors. Can be one of: cca: Canonical correlation analysis direct: Use assay data as a dimensional reduction
`bridge.assay.name`	Assay name used for bridge object reconstruction value (default is 'Bridge')
`reference.bridge.stored`	If refernece has stored the bridge dictionary representation
`k.anchor`	How many neighbors (k) to use when picking anchors
`k.score`	How many neighbors (k) to use when scoring anchors
`verbose`	Print messages and progress
`...`	Additional parameters passed to `FindIntegrationAnchors` or `FindTransferAnchors`