RunHarmony.SingleCellExperiment | R Documentation |
Applies harmony on PCA cell embeddings of a SingleCellExperiment.
## S3 method for class 'SingleCellExperiment'
RunHarmony(
object,
group.by.vars,
dims.use = NULL,
verbose = TRUE,
reduction.save = "HARMONY",
...
)
object |
SingleCellExperiment with the PCA reducedDim cell embeddings populated |
group.by.vars |
the name(s) of covariates that harmony will remove its effect on the data. |
dims.use |
a vector of indices that allows only selected cell embeddings features to be used. |
verbose |
enable verbosity |
reduction.save |
the name of the new slot that is going to be created by harmony. By default, HARMONY. |
... |
Arguments passed on to
|
SingleCellExperiment object. After running RunHarmony, the corrected cell embeddings can be accessed with reducedDim(object, "Harmony").
Other RunHarmony:
RunHarmony.Seurat()
,
RunHarmony.default()
,
RunHarmony()
## Not run:
## sce is a SingleCellExperiment R object
sce <- RunHarmony(sce, "donor_id")
## End(Not run)
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