Integrating pairs of samples separately in a Seurat object

[zhang248]

Hi,

I have a Seurat object with four samples named Heart-1, Heart-2, Liver-1, and Liver-2, which come from four distinct donors. Now I want to perform batch correction specifically for samples within the same tissue, namely Heart-1 and Heart-2, as well as Liver-1 and Liver-2.

In Seurat, I can identify all anchor pairs between each pair of these samples and then exclude the anchor pairs between heart and liver samples by subsetting the AnchorSet object. I'm wondering if there is a way to achieve the same using the RunHarmony function.

Thanks!