cell_pairing: Pair cells

In buenrostrolab/FigR: Functional Inference of Gene Regulation (FigR) using paired single cell ATAC-seq and RNA-seq data

Pair cells

Description

Perform geodesic pairing using ATAC/RNA co-embedding components

Usage

cell_pairing(
  ATACpcs,
  RNApcs,
  mode = "geodesic",
  tol = 1e-04,
  search_range = 0.2,
  max_multimatch = 5,
  umap_knn_k = 30,
  min_subgraph_size = 50,
  cca_umap_df = NULL,
  seed = 123
)

Arguments

ATACpcs	combined co-embedding components matrix of the ATAC cells. Must have valid ATAC cell barcode names as the rownames.
RNApcs	combined co-embedding components matrix of the RNA cells. Must have valid RNA cell barcode names as the rownames (unique from ATAC cell barcodes), and have the same number of components (columns) as the 'ATACpcs' matrix
mode	character specifying the pairing mode. Must be one of 'geodesic' (default) or 'greedy'.
tol	See fullmatch for more information on this parameter
search_range	This determines the size of the search knn window for allowed pairing. search_range * total number of cells = size of knn. Default is 0.2. Increasing this can take more time since we have to evaluate over more possible pairs
max_multimatch	Maximum number of cells in the larger dataset that is allowed to be matched to each cell in the smaller dataset (after up-sampling). Default is 5. This is only to allow for a solvable optmatch solution given geodesic constraints
umap_knn_k	Number of geodesic ATAC x RNA neighbors to consider in co-embedding graph
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.Default is 50 cells. Useful to set this to the smallest cell cluster size you might have in the data
cca_umap_df	optional umap of all ATAC+RNA cells to visualize UMAP of cells from each chunk being paired, colored by subgraph
seed	numeric specifying seed to use for subgraph UMAP and for down-sampling in case subgraphs are imbalanced

Value

a data.frame object containing ATAC and RNA cell barcodes from the resulting pairing

Author(s)

Yan Hu, Vinay Kartha

buenrostrolab/FigR documentation built on Feb. 10, 2023, 11:26 a.m.