PairCells.Rd
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: <vinay_kartha@g.harvard.edu>
Affiliation: Buenrostro Lab, Department of Stem Cell and Regenerative Biology, Harvard University
PairCells(
object,
reduction = NULL,
pair.by = NULL,
ident1 = "ATAC",
ident2 = "RNA",
assay = "RNA",
pair.mode = "geodesic",
tol = 1e-04,
search.range = 0.2,
max.multimatch = 5,
min_subgraph_size = 50,
seed = 42,
k = 300
)
The integrated Seurat object generated by the function CoembedData
Dimensional reduction to use for the pairing cells
Name of one metadata column to split the object for pairing;
Specify how to split the object, must be an value of pair.by
Specify how to split the object, must be an value of pair.by
Assay name based on which a KNN graph is constructed
Pair mode. Currently only "geodesic" is available
Tol times the number of subjects to be matched specifies the extent to which fullmatch's
This determines the size of the search knn. search_range * total number of cells = size of knn.
Maximum number of cells allowed to be matched to each cell
Minimum number of cells (ATAC/RNA each) needed for pairing in a given subgraph. Will skip subgraphs with fewer than these cells
Random seed
k-NN parameter used for applying constraints on ATAC-RNA pairs
A data frame containing the cell pairs
if (FALSE) {
df.pair <- PairCells(
object = obj.coembed,
reduction = "harmony",
pair.by = "tech",
ident1 = "ATAC",
ident2 = "RNA"
)
}