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


[Package CIDER version 0.99.1 Index]