is it possible to use clusterProfiler for CNVs?or is it only for differential expressed genes or chipseq?
It just uses lists of genes. If you can feed it a list of genes (e.g. those that are amplified), you can run it.
Thanks a lot for the answer.
On the other hand, would be correct to mix deleted and amplified genes? or better do them separately? I was thinking in the biological sense.
Depends on the question you're trying to answer. Mixing is appropriate if you just want to say a pathway is dysregulated, breaking them out into deletions and amplifications yields more information as to how said pathway is altered. If you have gene expression data, you could back up such statements with that data.
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