integration_workflow: Integration Workflow

In whtns/seuratTools: Tools for Managing Seurat Objects

Integration Workflow

Description

Integrate multiple seurat objects and save to file

Usage

integration_workflow(
  batches,
  excluded_cells = NULL,
  resolution = seq(0.2, 2, by = 0.2),
  experiment_name = "default_experiment",
  organism = "human",
  ...
)

Arguments

batches	seurat objects for all batches provided as a list. If named, the resulting integrated object will be identified with corresponding values in 'batch' metadata
excluded_cells	named list of cells to exclude
resolution	value(s) to control the clustering resolution via Seurat::FindMarkers
experiment_name	arbitrary name to identify experiment
organism	either "human" or "mouse"
...

Examples

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

integrated_seu <- integration_workflow(batches)

whtns/seuratTools documentation built on April 9, 2024, midnight