using scMerge2 with count matrix Seurat object

[martina811]

Hello everyone!
I would like to integrate 2 datasets of single cell using scMerge2. I have the two rds objects, coming from Seurat, containing the counts matrices for each dataset (genes on rows, cells on columns) how is it possible to use them for integration with scMerge ? How to combine them ?

Many thanks!

[DarioS]

SeuratObject merge will concatenate the columns of cells from two sources. Then, manually extract the combined matrix by allCounts <- LayerData(combined, assay = "RNA", layer = "counts"). Use log-allCounts for batch effect correction.