CID.smooth uses k-nearest neighbors to identify cells which
correspond to a different label than the majority of their first-degree neighbors. If so,
those annotations are "smoothed."
list containing a character vector where each element is a cell type or cell state assignment.
distance matrix (see ?CID.GetDistMat).
A character vector with smoothed labels
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## Not run: # load data classified previously (see SignacFast) P <- readRDS("celltypes.rds") S <- readRDS("pbmcs.rds") # get edges from default assay from Seurat object default.assay <- Seurat::DefaultAssay(S) edges = S@graphs[[which(grepl(paste0(default.assay, "_nn"), names(S@graphs)))]] # get distance matrix D = CID.GetDistMat(edges) # smooth labels smoothed = CID.smooth(ac = P$CellTypes, dM = D[]) ## End(Not run)
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