seurat_integration_pipeline: Run Seurat Integration

View source: R/pipeline.R

seurat_integration_pipelineR Documentation

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.