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.
I'm using the Seurat-wrappers
RunHarmony.Seurat,RunUMAP2,mapQuery,knnPredict.SeuratandbuildReferenceFromSeuratfor 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.Seuratwill be extremely slow as there are thousands of ATAC peaks.