In sampoll/rh5pydclient: Wrapper for python h5pyd package

knitr::opts_chunk$set(echo = TRUE)

Package

rh5pydclient is a R wrapper for the python package h5pyd.

library(rh5pydclient)

Initialization

The user must have a python executable, the R package reticulate and the python package h5pyd installed. The initPython initializes access to python and checks that h5pyd is installed. The user can set the path to the preferred python executable. By default, reticulate will search for a python executable to use.

initPython()

Connect to the server

Connect to a h5serv or hsds server and identify a H5 file to open.

conn <- initConn(domain='/home/stvjc/tenx_full.h5', mode='r', endpoint='http://52.4.181.237:5101')

Open a dataset

Obtain a handle to a dataset.

D <- getDataset(conn, 'newassay001')

Download data

At present, the only way to signify the submatrix to fetch is to pass slices as constant R strings in the format start:stop:step. The indices should be in R convention, i.e., the first array subscript is 1 (not 0) and if stop-start is a multiple of step, the index stop is included in the slice.

A <- getSubmatrix(D, c('200:300:1', '400:600:1'))
sum(A)    # should be 2848

sampoll/rh5pydclient documentation built on May 3, 2019, 3:41 p.m.