ReassignSmallClusters: ReassignSmallClusters

In jn-goe/gruffi: Gruffi identifies and removes stressed cells from brain organoid single-cell datasets.

ReassignSmallClusters

Description

Reassign granules (clusters) smaller than X to nearby granules based on 3D UMAP coordinates.

Usage

ReassignSmallClusters(
  obj = combined.obj,
  ident = obj@misc$gruffi$optimal.granule.res,
  cell.num = 30,
  reduction = c("pca", "3d_umap")[2],
  nr.of.PCs.for.3D.umap.computation = ncol(obj@reductions$[e-mail])
)

Arguments

obj	Seurat single cell object, Default: combined.obj
ident	Identity (granules / clustering) to reassign, Default: obj@misc$gruffi$optimal.granule.res
cell.num	Minimum number of cells per granule / cluster, Default: 30
reduction	Dim. reduction used to estimate closest cluster center when reassigning. Default: c("pca", "3d_umap")2
nr.of.PCs.for.3D.umap.computation	If 3D umap need to be recomputed, how many PCA-dimensions to be used?, Default: ncol(obj@reductions$[e-mail])

See Also

iprint RunUMAP, reexports

jn-goe/gruffi documentation built on Nov. 7, 2024, 10:38 p.m.