## ----setup, include=FALSE------------------------------------------------ knitr::opts_chunk$set(echo = TRUE) library(rhdf5client) ## ------------------------------------------------------------------------ src.hsds <- HSDSSource('http://hsdshdflab.hdfgroup.org') ## ------------------------------------------------------------------------ listDomains(src.hsds, '/home/jreadey') listDomains(src.hsds, '/home/jreadey/HDFLabTutorial') ## ------------------------------------------------------------------------ f0 <- HSDSFile(src.hsds, '/home/spollack/testzero.h5') f1 <- HSDSFile(src.hsds, '/shared/bioconductor/tenx_full.h5') ## ------------------------------------------------------------------------ listDatasets(f0) listDatasets(f1) ## ------------------------------------------------------------------------ d0 <- HSDSDataset(f0, '/grpA/grpAB/dsetX') d1 <- HSDSDataset(f1, '/newassay001') ## ------------------------------------------------------------------------ apply(getData(d1, c('1:4', '1:27998'), transfermode='JSON'), 1, sum) apply(getData(d1, c('1:4', '1:27998'), transfermode='binary'), 1, sum) ## ------------------------------------------------------------------------ apply(getData(d1, list(1:4, 1:27998), transfermode='JSON'), 1, sum) apply(getData(d1, list(1:4, 1:27998), transfermode='binary'), 1, sum) ## ------------------------------------------------------------------------ apply(d1[1:4, 1:27998], 1, sum)