Integrate scRNA-seq data using batch-balanced KNN (BBKNN)

This is a wrapper for BBKNN (https://github.com/Teichlab/bbknn). BBKNN is a fast and intuitive batch effect removal tool. It generates a BBKNN cell x cell similarity graph that can be used for clustering and UMAP embedding.

runBBKNN(
  object,
  batch,
  reduction = "pca",
  assay = DefaultAssay(object),
  do.umap = T,
  verbose = T
)

Arguments

object

Seurat object

batch

name of meta data field specifying batch groupings.

reduction

reduction used for batch correction. Default is "pca".

assay

assay name. Default is DefaultAssay(object).

do.umap

compute UMAP. Default is T.

verbose

print progress. Default is T.

Value

Seurat object with bbKNN-corrected UMAP stored in "b" reduction slot (if do.umap = T).

Author

Nicholas Mikolajewicz

Examples

 object <- runBBKNN(object, batch = "sample")
#> 2022-08-03 14:42:28: Checking inputs...
#> Error in "Seurat" %in% class(object): object 'object' not found