Big data takes too long for cells to pair

[liyang24]

hi! Thanks for this great work! Since this is the data of merge in three periods, and I was using so many cells, this step took so long to get nowhere

df.pair <- PairCells(object = coembed.sub, reduction = "harmony",pair.by = "tech", ident1 = "ATAC", ident2 = "RNA") Getting dimensional reduction data for pairing cells... Pairing cells using geodesic mode... Constructing KNN graph for computing geodesic distance .. Computing graph-based geodesic distance .. KNN subgraphs detected: 1 Skipping subgraphs with either ATAC/RNA cells fewer than: 50 Pairing cells for subgraph No.1 Total ATAC cells in subgraph: 26748 Total RNA cells in subgraph: 29030 Subgraph size: 26748 Search threshold being used: 10700 Constructing KNN based on geodesic distance to reduce search pairing search space Number of cells being paired: 26748 ATAC and 26748 RNA cells Determing pairs through optimized bipartite matching ..

I would like to know whether I can get the obj.pair of each period first and then merge them together

[lzj1769]

Hi @liyang24

Sure, you can run the PairCells function for each period individually, and then merge the paired cells afterward.

[liyang24]

Thanks! I got the merge obj now