CoembedData: Integrate data

In CostaLab/scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

Integrate data

Description

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

Usage

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

## Not run: 
obj.coembed <- CoembedData(
   obj.rna = obj.rna,
   obj.atac = obj.atac,
   gene.activity = gene.activity,
   weight.reduction = "harmony"
)


## End(Not run)

CostaLab/scMEGA documentation built on Sept. 25, 2024, 6:11 a.m.