seurat_integration_pipeline | R Documentation |
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/
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",
find_markers = TRUE,
...
)
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" |
... |
batches <- panc8 %>%
Seurat::SplitObject(split.by = "tech")
integrated_seu <- seurat_integration_pipeline(batches)
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