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The title is self-descriptive, so I will not dwell on the issue at length before showing the code. Just a small note: to my knowledge, there is only one public snippet out there that addresses this particular problem. It uses the Bioc package rhdf5 and you can find it here. The main problem is that it only works when the HDF5 file contains a single data frame, which is not very useful. This gist overcomes this limitation and uses the CRAN package h5 instead:
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