long vectors not supported for PairCells

[sallyqus]

Hi Team,

Thanks for the great work!

When I was trying to run the code for a bit larger dataset, I got this error for pairCells function:

> pairing <- pairCells(ATAC = ATAC_PCs,
+                      RNA = RNA_PCs,
+                      keepUnique = TRUE)
Running geodesic pairing in after chunking data ..
Number of cells in bigger dataset:  70012 
Number of cells in smaller dataset:  32929 
Difference in cell count between 2 datasets:  37083 
Chunking larger dataset to match smaller datset ..
Chunk size n =  32929  cells
Total number of chunks:  3 

Chunk #  1 
No. cells in chunk:  32929 



Constructing KNN graph for computing geodesic distance ..
Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted,  : 
  long vectors not supported yet: ../../src/include/Rinlinedfuns.h:537

Is it because of the large chunk size? Is it possible to provide a parameter to adjust the chunk size?

Thank you in advance for any of your help!

Best,
Sally

[vkartha]

Hi there - thanks for your interest in using this package. I have actually never run into this problem before, but it would make sense if the igraph dependency function was unable to support vectors that are that large to create an adjacency matrix. Let me see if I can add a chunkSize parameter such that it an support smaller divisions that might solve this problem.

[tianchen2019]

Hi there - thanks for your interest in using this package. I have actually never run into this problem before, but it would make sense if the igraph dependency function was unable to support vectors that are that large to create an adjacency matrix. Let me see if I can add a chunkSize parameter such that it an support smaller divisions that might solve this problem.

i also run into this probelm. I was wondering how do I handle this on my own?

[sharmasiddhartha231]

Hello. I am facing the same problem. Is there a workaround to this?

[OMIC-coding]

Hi. I'm also facing the same problem. Could you please upload a new version of FigR package with this issue being resolved?