Integrate scRNA-seq data using Scanorama

This is a wrapper for Scanorama (https://github.com/brianhie/scanorama). Scanorama enables batch-correction and integration of heterogeneous scRNA-seq datasets.

runScanorama(
  object,
  batch,
  do.umap = F,
  nfeatures = 2000,
  vars2regress = "percent.mt",
  dim = 50L,
  verbose = T
)

Arguments

object

Seurat object or list of seurat objects.

batch

name of meta data field specifying batch groupings.

do.umap

compute UMAP. Default is T.

nfeatures

number of features to use for integration. Default is 2000.

vars2regress

variable to regress out. Ignored if SCT assay is available in provided object.

dim

number of dimensions to use for integration. Default is 50L.

verbose

print progress. Default is T.

Value

Seurat object.

Author

Nicholas Mikolajewicz

Examples

 object <- runScanorama(object, batch = "sample")
#> 2022-08-03 14:42:30: Checking python modules...
#> Error in "SCT" %in% names(object@assays): object 'object' not found