Use Seurat rPCA to do batch correction. For more details on rPCA, see https://satijalab.org/seurat/articles/integration_rpca.html.
Arguments
- dat
NO DEFAULT. A data.table
- use.cols
NO DEFAULT. A vector of character column names to apply batch correction to.
- batch.col
Character. The column in the data in data.table that identifies which batch each cell belongs to.
- reference
DEFAULT NULL. Whether to align to batches to a given batch. If yes, then supply this parameter with the name of the batch you want to align the other batches to.
- k.anchor
DEFAULT 5. Passed to Seurat's FindIntegrationAnchors function. Essentially, it determines the number of neighbors (k) to use when Seurat's FindIntegrationAnchors is picking anchors.