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

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

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