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Merge initial clusters into final clusters based on the matrix of IDEr.
finalClustering( seu, dist, cutree.by = "h", cutree.h = 0.45, cutree.k = 3, hc.method = "complete" )
Seurat S4 object with final clustering results in `CIDER_clusters` of meta.data.
Seurat S4 object after the step of `getIDEr`. Required.
A list. Output of `getIDEr`. Required.
Character. Cut the tree by which parameter, height ("h") or number of clusters ("k"). (Default: h)
Numeric between 0 and 1. The height used to cut the tree. Ignored if `cutree.by = 'k`. (Default: 0.45)
Numeric/integer. Used to cut the tree. Ignored if `cutree.by = 'h`. (Default: 3)
Character. Used to choose the hierarchical clustering method.
getIDEr.
getIDEr
library(CIDER) data("pancreas") ider <- getIDEr(pancreas, downsampling.size = 30) seu <- finalClustering(pancreas, ider) head(seu$CIDER_cluster)
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