mergeInitialClusters {CIDER}

R Documentation

Merge Initial Clusters

Description

Merge Initial Clusters

Usage

mergeInitialClusters(
  seu_list,
  dist_list,
  use = "coef",
  method = "hc",
  hc.method = "average",
  cutree.by = "h",
  cutree.h = 0.6,
  cutree.k = 3
)

Arguments

seu_list	A list containing Seurat objects. Required.
dist_list	A list containing similarity matrices. The output of 'getDistMat ()'
use	Default: "coef". No other option available currently.
method	method = "hc"
hc.method	Passed to the 'method' parameter of 'hclust()'. Default: "average"
cutree.by	Cut trees by height ("h", default) or number of clusters ("k")
cutree.h	Height used to cut the tree. Default: 0.6.
cutree.k	Number of clusters used to cut the tree. Default: 3.

Value

a list of Seurat objects containing the updated initial clustering information in 'seu_list[[seu_itor]]$inicluster'. The original initial cluster information is stored in 'seu_list[[seu_itor]]$inicluster_tmp'.

See Also

hclust cutree gatherInitialClusters initialClustering

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