HSDSArray – DelayedArray backend for Remote HDF5

Samuela Pollack and others

Contents

1 Using the DelayedArray infrastructure

A remote dataset is accessed by giving the URL of the server, the type of the server (At present the only valid value is hsds.), the file domain (path to the HDF5 file) and the full path to the dataset inside the HDF5 file.

1.1 Interface to HSDS (HDF Object Store)

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

## <27998 x 1306127> matrix of class HSDSMatrix and type "double":
##                [,1]       [,2]       [,3] ... [,1306126] [,1306127]
##     [1,]          0          0          0   .          0          0
##     [2,]          0          0          0   .          0          0
##     [3,]          0          0          0   .          0          0
##     [4,]          0          0          0   .          0          0
##     [5,]          0          0          0   .          0          0
##      ...          .          .          .   .          .          .
## [27994,]          0          0          0   .          0          0
## [27995,]          1          0          0   .          0          0
## [27996,]          0          0          0   .          0          0
## [27997,]          0          0          0   .          0          0
## [27998,]          0          0          0   .          0          0

Again we have DelayedArray capabilities.

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

## [1] 4046 2087 4654 3193