Reintegrate (filtered) seurat objects

Source: R/seurat_integrate.R

  1. split by batch

  2. integrate

  3. run integration pipeline and save

reintegrate_seu(
  seu,
  feature = "gene",
  suffix = "",
  reduction = "pca",
  algorithm = 1,
  ...
)

Arguments

seu

A seurat object

suffix

to be appended to file saved in output dir

reduction

to use default is pca

Examples

panc8$batch <- panc8$gene$tech
#> Error in methods::slot(object = object, name = layer): no slot of name "tech" for this object of class "Assay"
reintegrate_seu(panc8)
#> Centering and scaling data matrix
#> Centering and scaling data matrix
#> Computing 2000 integration features
#> Scaling features for provided objects
#> Finding all pairwise anchors
#> Running CCA
#> Merging objects
#> Finding neighborhoods
#> Finding anchors
#> 	Found 1029 anchors
#> Filtering anchors
#> 	Retained 703 anchors
#> Merging dataset 2 into 1
#> Extracting anchors for merged samples
#> Finding integration vectors
#> Finding integration vector weights
#> Integrating data
#> Error in UseMethod(generic = "JoinLayers", object = object): no applicable method for 'JoinLayers' applied to an object of class "c('Assay', 'KeyMixin')"