I have some gene expression data which I would like to cluster using R.
I have a matrix of exon IDs (rows) and tissue names (columns) that I would like to cluster according to their expression values (data elements). However, the problem is that each exon id (e.g. 184049260_184049394_ENSG00000114867) belongs to a specific gene id (e.g. ENSG00000114867), and therefore I want to constrain the clustering so that the exons remain grouped according to their gene. The exons are allowed to cluster only within their gene group.
I came across an R package called flexclust which contains a method called k-centroids cluster analysis (kcca) which I thought might be useful. However, the documentation for kcca does not explain the function of each argument very well.
Does anyone know if there is package in R that is suitable for this task? And if so, could you explain how to implement it?