Apply Integration batch effect correction method from Seurat v3 to SingleCellExperiment object

Source: R/runSeurat3Integration.R

Can get either a full-sized corrected assay or a dimension reduced corrected matrix.

runSeurat3Integration(
  inSCE,
  useAssay = "logcounts",
  batch = "batch",
  altExpName = "Seurat3Int",
  nAnchors = nrow(inSCE),
  verbose = TRUE
)

Arguments

inSCE

SingleCellExperiment inherited object. Required.
useAssay

A single character indicating the name of the assay requiring batch correction. Default "logcounts".
batch

A single character indicating a field in colData that annotates the batches. Default "batch".
altExpName

A single character. The name for the altExp that stores the corrected assay. The name of this assay has the same name. Default "Seurat3Int".
nAnchors

An integer. The number of features to anchor. The final number of the corrected features depends on this value. Default nrow(inSCE).
verbose

A logical scalar. Whether to show detail information of the process. Default TRUE.

Value

The input SingleCellExperiment object with altExp(inSCE, altExpName) updated.

Details

This method aims to first identify anchors between pairs of datasets, that represent pairwise correspondences between individual cells in each dataset, that is hypothesized to originate from the same cell state. These anchors are then used to harmonize the datasets, or transfer information from one dataset to another.

References

Stuart et al. 2019

Examples

if (FALSE) {
data('sceBatches', package = 'singleCellTK')
sceCorr <- runSeurat3Integration(sceBatches, nAnchors = 100)
}