runSeuratIntegration: runSeuratIntegration A wrapper function to Seurat...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

runSeuratIntegration A wrapper function to Seurat Batch-Correction/Integration workflow.

Description

runSeuratIntegration A wrapper function to Seurat Batch-Correction/Integration workflow.

Usage

runSeuratIntegration(
  inSCE,
  useAssay = "counts",
  batch,
  newAssayName = "SeuratIntegratedAssay",
  kAnchor,
  kFilter,
  kWeight,
  ndims = 10
)

Arguments

inSCE	Input SingleCellExperiment object that contains the assay to batch-correct.
useAssay	Assay to batch-correct.
batch	Batch variable from colData slot of SingleCellExperiment object.
newAssayName	Assay name for the batch-corrected output assay.
kAnchor	Number of neighbours to use for finding the anchors in the FindIntegrationAnchors function.
kFilter	Number of neighbours to use for filtering the anchors in the FindIntegrationAnchors function.
kWeight	Number of neighbours to use when weigthing the anchors in the IntegrateData function.
ndims	Number of dimensions to use. Default 10.

Value

A SingleCellExperiment object that contains the batch-corrected assay inside the altExp slot of the object

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.