R/seuratFunctions.R
runSeuratIntegration.Rd
runSeuratIntegration A wrapper function to Seurat Batch-Correction/Integration workflow.
runSeuratIntegration(
inSCE,
useAssay = "counts",
batch,
newAssayName = "SeuratIntegratedAssay",
kAnchor,
kFilter,
kWeight,
ndims = 10
)
Input SingleCellExperiment
object that contains the assay
to batch-correct.
Assay to batch-correct.
Batch variable from colData
slot of
SingleCellExperiment
object.
Assay name for the batch-corrected output assay.
Number of neighbours to use for finding the anchors in the FindIntegrationAnchors function.
Number of neighbours to use for filtering the anchors in the FindIntegrationAnchors function.
Number of neighbours to use when weigthing the anchors in the IntegrateData function.
Number of dimensions to use. Default 10
.
A SingleCellExperiment
object that contains the
batch-corrected assay inside the altExp
slot of the object