seurat_integration_pipeline: Run Seurat Integration

In whtns/seuratTools: Tools for Managing Seurat Objects

Run Seurat Integration

Description

Run batch correction, followed by:

1. stashing of batches in metadata 'batch'

2. clustering with resolution 0.2 to 2.0 in increments of 0.2

3. saving to <proj_dir>/output/sce/seu.rds

Usage

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,
  ...
)

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)

whtns/seuratTools documentation built on Oct. 28, 2024, 7:18 a.m.