mergeInitialClusters {CIDER} | R Documentation |
Merge Initial Clusters
mergeInitialClusters(
seu_list,
dist_list,
use = "coef",
method = "hc",
hc.method = "average",
cutree.by = "h",
cutree.h = 0.6,
cutree.k = 3
)
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. |
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'.
hclust
cutree
gatherInitialClusters
initialClustering