Integrate data

This function wraps a number of functions from the Seurat package. It integrates and projects the single-cell multi-omics (e.g., scRNA-seq and scATAC-seq) data into a common low-dimensional space via CCA approach. The details can be found: https://satijalab.org/seurat/articles/seurat5_atacseq_integration_vignette

CoembedData(
  obj.rna,
  obj.atac,
  gene.activity,
  reference.assay = "RNA",
  reduction = "cca",
  weight.reduction = NULL,
  verbose = TRUE,
  dims = 1:30
)

Arguments

obj.rna

A Seurat object including gene expression data

obj.atac

A Seurat object including chromatin accessibility data

gene.activity

A sparse matrix containing gene activity score per cell

reference.assay

The reference assay from gene expression data

reduction

The reduction name used for function FindTransferAnchors.

weight.reduction

Dimensional reduction to use for the weighting anchors

verbose

Print progress bars and output

dims

Set of dimensions to use in the anchor weighting procedure.

Value

An integrated Seurat object

Examples

if (FALSE) {
obj.coembed <- CoembedData(
   obj.rna = obj.rna,
   obj.atac = obj.atac,
   gene.activity = gene.activity,
   weight.reduction = "harmony"
)

}