Is There A Way To Perform Semi-Supervised Hierarchical Clustering In R?

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11.3 years ago

blakeleyp ▴ 20

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?

clustering r gene-expression • 3.3k views

ADD COMMENT • link 11.3 years ago by blakeleyp ▴ 20

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Do you want to cluster the tissues based on their expression? Or cluster the exons?

ADD REPLY • link 11.3 years ago by Chris Cabanski ▴ 330

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I would like to do both. But I am more interested in clustering the exons.

ADD REPLY • link 11.3 years ago by blakeleyp ▴ 20

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