In sampoll/rhdf5client2: Reorganization of rhdf5client code

suppressPackageStartupMessages({
suppressMessages({
library(rhdf5client2)
library(DelayedArray)
})
})

Using the DelayedArray infrastructure

A remote dataset is accessed by giving the URL of the server, the type of the server (either hsds or h5serv), the file domain (path to the HDF5 file) and the full path to the dataset inside the HDF5 file.

Interface to h5serv (Channing Remote Data Server)

da <- HSDSArray('http://h5s.channingremotedata.org:5000', 'h5serv', 
      'tenx_full.h5s.channingremotedata.org', '/newassay001')
da

Here we have defined the R image of the data to be the transpose of the image in HDF5. So neurons are columns.

apply(da[,1:4],2,sum)

Interface to HSDS (HDF Object Store)

da <- HSDSArray('http://hsdshdflab.hdfgroup.org', 'hsds', 
      '/shared/bioconductor/tenx_full.h5', '/newassay001')
da

Again we have DelayedArray capabilities.

apply(da[,1:4],2,sum)

sampoll/rhdf5client2 documentation built on May 24, 2019, 2:47 p.m.