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Seurat vignette (bottom of the page): https://satijalab.org/seurat/articles/multimodal_reference_mapping
query.batches <- SplitObject(query, split.by = "sampleid") #query.batches <- lapply(X = query.batches, FUN = SCTransform, verbose = FALSE) # from Seurat vignette #modified version for (i in 1:length(query.batches)) { print(i) query.batches[[i]] <- SCTransform(query.batches[[i]], assay="RNA", residual.features = rownames(x = reference), method = 'glmGamPoi', ncells = 4000, n_genes = 5000, vars.to.regress = "percent.mt", do.correct.umi = FALSE, do.scale = FALSE, do.center = TRUE, verbose = FALSE) } anchors <- list() for (i in 1:length(query.batches)) { anchors[[i]] <- FindTransferAnchors( reference = reference, query = query.batches[[i]], normalization.method = "SCT", # recompute.residuals=FALSE, reference.reduction = "spca", k.filter = NA, dims = 1:15 ) } for (i in 1:length(query.batches)) { query.batches[[i]] <- MapQuery( anchorset = anchors[[i]], query = query.batches[[i]], reference = reference, refdata = list( celltype = "celltype.l2", predicted_ADT = "ADT"), reference.reduction = "spca", reduction.model = "wnn.umap" ) } for (i in 1:length(query.batches)) { query.batches[[i]] <- AddMetaData( object = query.batches[[i]], metadata = MappingScore(anchors = anchors[[i]]), col.name = "mapping.score" ) } # Merge the batches query <- merge(query.batches[[1]], query.batches[2:length(query.batches)], merge.dr = "ref.umap") query
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Seurat vignette (bottom of the page): https://satijalab.org/seurat/articles/multimodal_reference_mapping
The text was updated successfully, but these errors were encountered: