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argument 3 matches multiple formal arguments #253

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jasoncrucify opened this issue Jul 11, 2024 · 0 comments
Open

argument 3 matches multiple formal arguments #253

jasoncrucify opened this issue Jul 11, 2024 · 0 comments

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@jasoncrucify
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hi,
Error in RunHarmony.Seurat(object = merged_seurat, group.by.var = "orig.ident", :
argument 3 matches multiple formal arguments

when I run seurat <- harmony::RunHarmony(object =seurat, group.by.vars="orig.ident",
reduction = "pca", assay.use="RNA", plot_convergence = T, verbose = T)

when I removed reduction = "pca", it worked, but the harmony dimension drops to 4, no idea what happened, it seems the harmony integration worked

seurat was from a merged seurat object from two seurat object by merging a group of sample of each.

do you know what happened the error?

many thanks

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