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immunogenomics / harmony

Fast, sensitive and accurate integration of single-cell data with Harmony
https://portals.broadinstitute.org/harmony/
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Integration of scATACseq datasets #244

Closed pobmmu closed 6 months ago

pobmmu commented 6 months ago

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 commented 6 months ago

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