[BioC] Reading by column

pep pepmadon at gmail.com
Fri Aug 8 19:07:16 CEST 2014


My name is Carl I was hoping to get a little insight on reading columns 
using rhdf5

https://stat.ethz.ch/pipermail/bioconductor/2014-January/057047.html

Wayn's solution was to use pytables in python which is fine but does not 
address the issue of using rdhf5 and R.


IN R I get:

h5read(file="/home/pep/Downloads/tutorial1.h5", name="detector/readout", 
index=list(1:8 ))


index list gets me rows and columns 8x8



   ADCcount TDCcount  energy grid_i grid_j   idnumber name pressure
1        0        0       0      0     10          0 Particle: 0        0
2      256        1       1      1      9 2147483647 Particle: 1        1
3      512        2     256      2      8 2147483647 Particle: 2        4
4      768        3    6561      3      7 2147483647 Particle: 3        9
5     1024        4   65536      4      6 2147483647 Particle: 4       16
6     1280        5  390625      5      5 2147483647 Particle: 5       25
7     1536        6 1679616      6      4 2147483647 Particle: 6       36
8     1792        7 5764801      7      3 2147483647 Particle: 7       49


h5read(file="/home/pep/Downloads/tutorial1.h5", name="detector/readout", 
index=list(1:7 ))

NOW index list gets me rows and columns 7x7


   ADCcount TDCcount  energy grid_i grid_j   idnumber name
1        0        0       0      0     10          0 Particle: 0
2      256        1       1      1      9 2147483647 Particle: 1
3      512        2     256      2      8 2147483647 Particle: 2
4      768        3    6561      3      7 2147483647 Particle: 3
5     1024        4   65536      4      6 2147483647 Particle: 4
6     1280        5  390625      5      5 2147483647 Particle: 5
7     1536        6 1679616      6      4 2147483647 Particle: 6

how do I get rows and columns?
10 rows column 3
10 rows column energy


Any help would be appreciated I cannot find any documentation.



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