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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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argument 3 matches multiple formal arguments #255

Closed Guliariel closed 6 days ago

Guliariel commented 2 months ago

Hello I am trying to runHArmony for a merged Seurat object (scATAC-like data). I am using this command: MYSEURATOBJ <- RunHarmony(object = MYSEURATOBJ, group.by.vars = 'dataset', reduction = 'lsi', assay.use = 'bins', project.dim = FALSE).

I receive this error: argument 3 matches multiple formal arguments

I would appreciate your suggestion how to solve this issue. Thank you

pati-ni commented 2 months ago

There are two different arguments, reduction.use and reduction.save and this is the reason you are getting this error. You need to reduction.use='lsi'

On Thu, Aug 15, 2024, 20:02 Guliariel @.***> wrote:

Hello I am trying to runHArmony for a merged Seurat object (scATAC-like data). I am using this command: MYSEURATOBJ <- RunHarmony(object = MYSEURATOBJ, group.by.vars = 'dataset', reduction = 'lsi', assay.use = 'bins', project.dim = FALSE).

I receive this error: argument 3 matches multiple formal arguments

I would appreciate your suggestion how to solve this issue. Thank you

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