[BioC] Reading by column

[Nathaniel Hayden]

Hi, Wayne. Did you find what you needed for your subsetting scenario? 
I'm not very familiar with rhdf5 myself, but the documentation addresses 
subsetting for reads and writes by any number of dimensions, using the 
index argument. See section 3.3 of the rhdf5 vignette.
On 01/08/2014 12:09 PM, Hajas, Wayne wrote:
> This is likely a simple question - but I couldn't find a similar problem
> in the archives.
>
>   
>
> I am trying to use rhdr5 to read a .hdf5 file of a pre-determined
> structure.  My problem is that I am generating a table of values that is
> going to grow very large.  So far, I can only figure out how to read the
> entire table at once.  Eventually, I expect my table to be 800 x 100000
> so I will need to be able to go one column at a time.
>
>   
>
> Here is an example.
>
>   
>
>> typeof(h5read(HDF5file,"chain0/PyMCsamples"))
> [1] "list"
>
>   
>
> One of the columns in the dataframe (elements in the list) is named
> 'deviance'.
>
>   
>
>> length(h5read(HDF5file,"chain0/PyMCsamples")$deviance)
> [1] 47
>
>   
>
> I would like to be able to do something like:
>
>   
>
>> h5read(HDF5file,"chain0/PyMCsamples/deviance")
> Error in h5read(HDF5file, "chain0/PyMCsamples/deviance") :
>
>    Object chain0/PyMCsamples/deviance does not exist in this HDF5 file.
>
>   
>
> Can anyone point me in the right direction?
>
> Thanks very much,
>
> Wayne Hajas
>
>   
>
>
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>
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