How to extract the subcluster based on PCC (pearson correlation coefficient) in Hierarchical Clustering ?
Hi, company, I am doing a Hierarchical Clustering with a gene expression data based on PCC (Pearson correlation coefficient), and want to extract the subcluster whose sum of PCC is the highest, I know cutree() can help me extract subgroup, however, how to output the highest PCC group? Any ideas? Thank you very much! BTW, here is my cluster code:
hc_w2=hclust(as.dist( 1-cor(t(clu_w2),method = "pearson")),method = "complete")
• 2,325 views
•
link
updated
by
Kevin Blighe
•
written
by
BioLite •
•
written
by
BioLite •
1 answer
Take a look at my answers, here:
- A: extract dendrogram cluster from pheatmap
- A: How can I get the ordered names or new matrix according to cluster result?
You want to use:
cutree(MyTree, h=0.7) # cut at height 0.7
Kevin
• 1 views
•
link
written
by
Kevin Blighe
Log in to answer this question.
More posts like this
-
hclust with similar data gives different
written by Harish.Sudarsanam •
-
How to make cut off linein cluster,
written by Info.shi •
-
Extract differentially expressed genes list from DESeq2 results for each of the sample provided
written by Lawrence •
-
Why are gene expression phylogenies and the structure of hierarchical clustering so different?
written by haoyan14ioz •
-
pheatmap vs. manual hclust with different results
written by sdominguez •
-
cluster based on full dataset but only show heatmap for 4 genes
written by Ron
-
Extract Dendrogram Information From Heatmap Generated By Heatmap.2
written by Ming Tommy Tang
-
Hierarchical Clustering Based On Gene Expression Values
written by APJ •
-
Gene Expression Data Hierarchical Clustering, Plot Heat Map With Ggplot
written by k.nirmalraman
-
Comparing Clusters From The Dendrogram Using R Programming?
written by Mkl •
Maybe I can use cutree() extract every subgroup, and then calculate their PCC summations then making a comparison? But this doesn't like the best method?