seuratIntegration {singleCellTK} | R Documentation |
seuratIntegration A wrapper function to Seurat Batch-Correction/Integration workflow.
seuratIntegration( inSCE, useAssay = "counts", batch, newAssayName = "SeuratIntegratedAssay", kAnchor, kFilter, kWeight, ndims = 10 )
inSCE |
Input |
useAssay |
Assay to batch-correct. |
batch |
Batch variable from |
newAssayName |
Assay name for the batch-corrected ouput 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 |
A SingleCellExperiment
object that contains the batch-corrected assay inside the altExp
slot of the object