MergeSeuratObjs: MergeSeuratObjs

In bimberlabinternal/OOSAP: OHSU-ONPRC Single-cell Analysis Package

Description

Merges a list of Seurat objects, using Seurat::IntegrateData()

Usage

MergeSeuratObjs(
  seuratObjs,
  metadata = NULL,
  method = c("simple", "cca"),
  maxCCAspaceDim = 20,
  maxPCs2Weight = 20,
  useAllFeatures = F,
  nVariableFeatures = 2000,
  includeCellCycleGenes = T,
  assay = NULL,
  normalization.method = "LogNormalize",
  spike.genes = NULL,
  spikeImmuneGenes = T
)

Arguments

seuratObjs	A list of seurat objects, optionally named (in which case these will be used as dataset names). Also can use SplitObject(, split.by =)
metadata	A list of metadata. If provided, the names of this list will be used as dataset names
method	A string either simple or cca
maxCCAspaceDim	The number of dims to use with FindIntegrationAnchors()
maxPCs2Weight	The number of dims to use with IntegrateData()
useAllFeatures	If true, the resulting object will contain all features, as opposed to just VariableGenes (not recommended due to complexity). Also having all genes, means possibly more unwanted noise. Consider Spiking interesting/canonical genes as oppose to all.
nVariableFeatures	The number of VariableFeatures to identify
includeCellCycleGenes	If true, the cell cycles genes will always be included with IntegrateData(), as opposed to just VariableGenes
assay	The assay to use
normalization.method	Normalization method
spike.genes	If CCA is used, this list of list of genes will be spiked into the merged object, beyond the default VariableGenes()
spikeImmuneGenes	If CCA is used, this will spike a pre-determined set of immune-related genes into the merged object
projectName	The project name when creating the final seuratObj

Value

A modified Seurat object.

bimberlabinternal/OOSAP documentation built on Jan. 19, 2021, 2:47 a.m.