dynamic tree cut

Question

[druggable]

Hi,

I am clustering log2fold changes of genes. I am confused about the output of the dynamictreecut package. If I run the following:

dynamic_hybrid = cutreeHybrid(clust_fc, as.matrix(dist_fc), deepSplit=1)
clusters = dynamic_hybrid$labels

how do I know which genes are assigned to which clusters? Will the ordering of cluster assignment to genes be rownames of the input clust_fc?

In other words, what is the proper way of extracting the cluster assignment for each gene in the clustering?

Thank you very much.

teabonng

Answer 1

[Jean-Karim Heriche]

As per the docs for cutreeHybrid(), the function returns a list in which one element is called labels and contains the cluster assignments, i.e. a cluster indicator vector C such that C[i] = k means item i belongs to cluster k.