RunHarmony.Seurat | R Documentation |
Applies harmony on a Seurat object cell embedding.
## S3 method for class 'Seurat'
RunHarmony(
object,
group.by.vars,
reduction.use = "pca",
dims.use = NULL,
reduction.save = "harmony",
project.dim = TRUE,
...
)
object |
the Seurat object. It needs to have the appropriate slot of cell embeddings precomputed. |
group.by.vars |
the name(s) of covariates that harmony will remove its effect on the data. |
reduction.use |
Name of dimension reduction to use. Default is pca. |
dims.use |
indices of the cell embedding features to be used |
reduction.save |
the name of the new slot that is going to be created by harmony. By default, harmony. |
project.dim |
Project dimension reduction loadings. Default TRUE. |
... |
Arguments passed on to
|
Seurat object. Harmony dimensions placed into a new slot in the Seurat object according to the reduction.save. For downstream Seurat analyses, use reduction='harmony'.
Other RunHarmony:
RunHarmony.SingleCellExperiment()
,
RunHarmony.default()
,
RunHarmony()
## Not run:
## seu is a Seurat single-Cell R object
seu <- RunHarmony(seu, "donor_id")
## End(Not run)
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