Integration of scATACseq datasets

[pobmmu]

Hello,

I am having trouble to integrate two scATACseq datasets with Harmony. I get this error message:

merged.harmony <- RunHarmony(merged, group.by.vars = "dataset", reduction = "lsi", assay.use = "ATAC", project.dim = FALSE)
Error in RunHarmony.Seurat(merged, group.by.vars = "dataset", reduction = "lsi", :
argument 3 matches multiple formal arguments

I have created a common peak set before merging the datasets with the merge() function.

[pobmmu]

actually I found that using reduction.use = "lsi" solved the problem