[BioC] Error working with indexes in htf5 files

Maria Pedroto [guest] guest at bioconductor.org
Wed Apr 2 19:49:31 CEST 2014


Hello,
I'm trying to use the rhdf5 package to read and iterate in a hdf5 database. 
The structure of the database is of a simple table of 13 columns with two of them being indexes.

I'm not being able to find out how to use the indexes to find the information I need. That is, I think i need to access the timestamp index and return a value to be inserted in the h5read function at the index field. 

Dunnow if i'm using the best function because I haven't found on the web an example so complicated. 

Best regards,
Maria Pedroto

 -- output of sessionInfo(): 

h5ls(filename, datasetinfo=TRUE)
                  group      name       otype   dclass           dim
0                     / _i_events   H5I_GROUP                       
1            /_i_events    msisdn   H5I_GROUP                       
2     /_i_events/msisdn   abounds H5I_DATASET  INTEGER        105408
3     /_i_events/msisdn    bounds H5I_DATASET  INTEGER     287 x 366
4     /_i_events/msisdn   indices H5I_DATASET  INTEGER 4718592 x 366
5     /_i_events/msisdn indicesLR H5I_DATASET  INTEGER       4718592
6     /_i_events/msisdn   mbounds H5I_DATASET  INTEGER        105408
7     /_i_events/msisdn   mranges H5I_DATASET  INTEGER           366
8     /_i_events/msisdn    ranges H5I_DATASET  INTEGER       2 x 366
9     /_i_events/msisdn    sorted H5I_DATASET  INTEGER 4718592 x 366
10    /_i_events/msisdn  sortedLR H5I_DATASET  INTEGER       4718881
11    /_i_events/msisdn   zbounds H5I_DATASET  INTEGER        105408
12           /_i_events timestamp   H5I_GROUP                       
13 /_i_events/timestamp   abounds H5I_DATASET   STRING        105408
14 /_i_events/timestamp    bounds H5I_DATASET   STRING     287 x 366
15 /_i_events/timestamp   indices H5I_DATASET  INTEGER 4718592 x 366
16 /_i_events/timestamp indicesLR H5I_DATASET  INTEGER       4718592
17 /_i_events/timestamp   mbounds H5I_DATASET   STRING        105408
18 /_i_events/timestamp   mranges H5I_DATASET   STRING           366
19 /_i_events/timestamp    ranges H5I_DATASET   STRING       2 x 366
20 /_i_events/timestamp    sorted H5I_DATASET   STRING 4718592 x 366
21 /_i_events/timestamp  sortedLR H5I_DATASET   STRING       4718881
22 /_i_events/timestamp   zbounds H5I_DATASET   STRING        105408
23                    /    events H5I_DATASET COMPOUND    1729572595

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