PairCells: Pair the cells

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

Pair the cells

Description

This function will create the pairs of cells between different modalities based on the integrated data generated by CoembedData. It was modified from https://github.com/buenrostrolab/stimATAC_analyses_code/blob/master/R/optMatching_functions.R to use Seurat object as input.
Author: Vinay Kartha, Yan Hu
Contact: <[e-mail]>
Affiliation: Buenrostro Lab, Department of Stem Cell and Regenerative Biology, Harvard University

Usage

PairCells(
  object,
  reduction = NULL,
  pair.by = NULL,
  ident1 = "ATAC",
  ident2 = "RNA",
  assay = "RNA",
  pair.mode = "greedy",
  tol = 1e-04,
  search.range = 0.2,
  max.multimatch = 5,
  min_subgraph_size = 50,
  seed = 42,
  k = 300
)

Arguments

object	The integrated Seurat object generated by the function CoembedData
reduction	Dimensional reduction to use for the pairing cells
pair.by	Name of one metadata column to split the object for pairing;
ident1	Specify how to split the object, must be an value of pair.by
ident2	Specify how to split the object, must be an value of pair.by
assay	Assay name based on which a KNN graph is constructed
pair.mode	Pair mode. Available options are: "greedy" and "geodesic".
tol	Tol times the number of subjects to be matched specifies the extent to which fullmatch's
search.range	This determines the size of the search knn. search_range * total number of cells = size of knn.
max.multimatch	Maximum number of cells allowed to be matched to each cell
min_subgraph_size	Minimum number of cells (ATAC/RNA each) needed for pairing in a given subgraph. Will skip subgraphs with fewer than these cells
seed	Random seed
k	k-NN parameter used for applying constraints on ATAC-RNA pairs

Value

A data frame containing the cell pairs

Examples

## Not run: 
df.pair <- PairCells(
  object = obj.coembed,
  reduction = "harmony",
  pair.by = "tech",
  ident1 = "ATAC",
  ident2 = "RNA"
  )

## End(Not run)

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