run.rpca: Run rPCA for batch correction
In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis

run.rpca

R Documentation

Run rPCA for batch correction

Use Seurat rPCA to do batch correction. For more details on rPCA, see https://satijalab.org/seurat/articles/integration_rpca.html.

run.rpca(dat, use.cols, batch.col, reference = NULL, k.anchor = 5)

`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.