[BioC] Reading by column

[Hajas, Wayne]

Thanks for asking Nathaniel!

Yours is the first response and I haven't had any luck plugging away on
my own.  I tried chunking as described in 3.3 but didn't get anywhere.

At, the end of this message, I will attach another example of what is
happening for me.  Any suggestions are appreciated,
Wayne


> 
> class(  h5read(HDF5file,"chain0/PyMCsamples") )
[1] "data.frame"
> dim(    h5read(HDF5file,"chain0/PyMCsamples") )
[1] 1000  828
> 
> h5read(HDF5file,"chain0/PyMCsamples",index=list(2:3,c(1,2,4,5)))
Error in h5read(HDF5file, "chain0/PyMCsamples", index = list(2:3, c(1,
: 
  length of index has to be equal to dimensional extension of HDF5
dataset.
>  
> 


-----Original Message-----
From: Nathaniel Hayden [mailto:nhayden at fhcrc.org] 
Sent: January-14-14 1:12 PM
To: Hajas, Wayne; bioconductor at r-project.org
Subject: Re: [BioC] Reading by column

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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