PerformIntegration: PerformIntegration

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

PerformIntegration

Description

This perform's Seurat's integration on a dataset

Usage

PerformIntegration(
  seuratObj,
  splitField = "SubjectId",
  nVariableFeatures = 4000,
  nIntegrationFeatures = 3500,
  k.weight = 20,
  dimsToUse = 20,
  integrationFeaturesInclusionList = NULL,
  integrationFeaturesExclusionList = NULL,
  minCellsPerSubsetObject = 75,
  dropGroupsBelowThreshold = TRUE
)

Arguments

seuratObj	A Seurat object.
splitField	The metadata field on which to split the seurat object for integration
nVariableFeatures	The number of variable features used for Seurat::FindVariableFeatures
nIntegrationFeatures	The number of features for Seurat::SelectIntegrationFeatures
k.weight	Passed to Seurat::IntegrateData()
dimsToUse	Passed to Seurat::IntegrateData(), as dims = 1:dimsToUse
integrationFeaturesInclusionList	An optional vector of genes that will be included in the integration genes
integrationFeaturesExclusionList	An optional vector of genes that will be excluded in the integration genes
minCellsPerSubsetObject	If any of the seurat objects after splitting on splitField have fewer than this many cells, they are either discarded or the function will throw an error, depending on dropGroupsBelowThreshold
dropGroupsBelowThreshold	If any of the seurat objects after splitting are below minCellsPerSubsetObject and if this param is true, they will be discarded.

Value

A modified Seurat object.

bimberlabinternal/CellMembrane documentation built on Dec. 25, 2024, 8:10 a.m.