finalClustering {CIDER}R Documentation

Final clustering step for meta-clustering

Description

Merge initial clusters into final clusters based on the matrix of IDEr.

Usage

finalClustering(
  seu,
  dist,
  cutree.by = "h",
  cutree.h = 0.45,
  cutree.k = 3,
  hc.method = "complete"
)

Arguments

seu

Seurat S4 object after the step of 'getIDEr'. Required.

dist

A list. Output of 'getIDEr'. Required.

cutree.by

Character. Cut the tree by which parameter, height ("h") or number of clusters ("k"). (Default: h)

cutree.h

Numeric between 0 and 1. The height used to cut the tree. Ignored if ‘cutree.by = ’k'. (Default: 0.45)

cutree.k

Numeric/integer. Used to cut the tree. Ignored if ‘cutree.by = ’h'. (Default: 3)

hc.method

Character. Used to choose the hierarchical clustering method.

Value

Seurat S4 object with final clustering results in 'CIDER_clusters' of meta.data.

See Also

getIDEr.

Examples

library(CIDER)
data("pancreas")
ider <- getIDEr(pancreas, downsampling.size = 30)
seu <- finalClustering(pancreas, ider)
head(seu$CIDER_cluster)

[Package CIDER version 0.99.1 Index]