Transfer entire assay / expression matrix from reference onto query

[MalteThodberg]

I'm using the Seurat-wrappers RunHarmony.Seurat, RunUMAP2, mapQuery, knnPredict.Seurat and buildReferenceFromSeurat for doing multi-modal (matched scRNA-Seq & scATAC-Seq) reference mapping with Symphony.

I can transfer a single label/column from the metadata of the multi-modal data to a unimodal scRNA dataset with knnPredict.Seurat.

I also want to transfer the entire ATAC assay from the multimodal reference onto the unimodal scRNA dataset, essentially imputing the missing scATAC modality for the scRNA dataset.

Is there a way to do this?

Transferring one ATAC peak at a time using knnPredict.Seurat will be extremely slow as there are thousands of ATAC peaks.