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Commit 1b63ad4f authored by Lars Velten's avatar Lars Velten
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R/RNAMagnet.R
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...@@ -84,7 +84,7 @@ RNAMagnetSignaling <- function(seurat, neighborhood.distance = NULL, neighborhoo ...@@ -84,7 +84,7 @@ RNAMagnetSignaling <- function(seurat, neighborhood.distance = NULL, neighborhoo
RNAMagnetBase <- function(seurat, anchors=NULL,neighborhood.distance=NULL, neighborhood.gradient =NULL, .k = 10, .x0 = 0.5, .minExpression, .version = "latest", .cellularCompartment, .manualAnnotation = "Correct", .symmetric = F) { RNAMagnetBase <- function(seurat, anchors=NULL,neighborhood.distance=NULL, neighborhood.gradient =NULL, .k = 10, .x0 = 0.5, .minExpression, .version = "latest", .cellularCompartment, .manualAnnotation = "Correct", .symmetric = F) {
cat("Setting everything up...\n") cat("Setting everything up...\n")
if (grepl("^3", Biobase::package.version("Seurat")) { if (grepl("^3", Biobase::package.version("Seurat"))) {
seurat.ident <- Idents(seurat) seurat.ident <- Idents(seurat)
seurat.cell.names <- colnames(seurat) seurat.cell.names <- colnames(seurat)
seurat.pca <- Embeddings(seurat, reduction = "pca") seurat.pca <- Embeddings(seurat, reduction = "pca")
......
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