MergeSeuratObjs: Merge Seurat Objects

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

Merge Seurat Objects

Description

Merges a list of Seurat objects

Usage

MergeSeuratObjs(
  seuratObjs,
  projectName,
  merge.data = FALSE,
  expectedDefaultAssay = "RNA",
  excludedAssays = c("UCellRanks"),
  enforceUniqueCells = TRUE,
  errorOnBarcodeSuffix = FALSE,
  doGC = FALSE,
  duplicateBarcodeMode = "exclude-all"
)

Arguments

seuratObjs	A named list of seurat objects, optionally named (in which case these will be used as dataset names).
projectName	The project name when creating the final seurat object
merge.data	Passed directly to Seurat::merge
expectedDefaultAssay	If not null, the DefaultAssay on the resulting seurat object will be set to this
excludedAssays	An optional list of assay names to drop prior to merge.
enforceUniqueCells	If true, all inputs must have unique cellbarcodes.
errorOnBarcodeSuffix	In certain cases, software appends a digit (i.e. -1) to the end of cellbarcodes. These can be a problem when trying to make string comparisons. If true, the method will error if these are encountered.
doGC	If true, in an attempt to save memory gc() will be run after each seurat object is merged
duplicateBarcodeMode	This dictates the behavior when duplicate cell barcodes are encountered between merged objects. This can be either: 'exclude-all' (all duplicated dropped from all objects), or 'error'.

Value

A modified Seurat object.

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.