Run Seurat Integration — seurat_integration

Run batch correction, followed by:

stashing of batches in metadata 'batch'
clustering with resolution 0.2 to 2.0 in increments of 0.2
saving to <proj_dir>/output/sce/seu.rds

seurat_integration_pipeline(
  seu_list,
  resolution = seq(0.2, 2, by = 0.2),
  suffix = "",
  algorithm = 1,
  organism = "human",
  annotate_cell_cycle = FALSE,
  annotate_percent_mito = FALSE,
  reduction = "pca",
  ...
)

Arguments

seu_list: List of seurat objects to be integrated
resolution: Range of resolution
suffix: a suffix to be appended to a file save in output dir
algorithm: Algorithm for modularity optimization. Default 1:original Louvain algorithm
organism: Default "human"
...

Examples


batches <- panc8 %>%
    Seurat::SplitObject(split.by = "tech")

integrated_seu <- seurat_integration_pipeline(batches)
#> 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')"