DelayedHDF5SMatrix-class: define container for H5S_dataset to use Delayed* interfaces

In vjcitn/RemoteArray: Delayed?Array with remote, e.g., HDF5Server or BigQuery, back end

Description

define container for H5S_dataset to use Delayed* interfaces

define a dim getter for H5S_dataset

define a dim getter for DelayedHDF5SMatrix

define dimnames operations for DelayedHDF5SMatrix

define dimnames setter for DelayedHDF5SMatrix

define subset_seed_as_array, key infrastructure for Delayed* seed

define bracket

constructor

printer

Usage

## S4 method for signature 'H5S_dataset'
dim(x)

## S4 method for signature 'DelayedHDF5SMatrix'
dim(x)

## S4 method for signature 'DelayedHDF5SMatrix'
dimnames(x)

## S4 replacement method for signature 'DelayedHDF5SMatrix'
dimnames(x) <- value

## S4 method for signature 'H5S_dataset'
subset_seed_as_array(seed, index)

## S4 method for signature 'DelayedHDF5SMatrix,ANY,ANY'
x[i, j, ..., drop = TRUE]

DelayedHDF5SMatrix(x, dimnames = list(NULL, NULL))

## S4 method for signature 'DelayedHDF5SMatrix'
show(object)

Arguments

x	instance of H5S_dataset-class
value	a list of dimnames
seed	instance of H5S_dataset
index	list
i	selection vector or missing
j	selection vector or missing
...	not used
drop	logical ignored for now
dimnames	list or missing
object	instance of DelayedHDF5SMatrix-class

Slots

seed

instance of H5S_dataset

dimnames

list

Examples

library(rhdf5client)
if (!exists("bigec2")) example(H5S_source) # minimize hits to server
ds = bigec2[["assays"]] # methylation data
dem = DelayedHDF5SMatrix( ds )
dem
subset_seed_as_array(dem@seed, list(1:3, 1:4))
library(restfulSE)
data(banoSEMeta)
library(SummarizedExperiment)
assays(banoSEMeta)
assays(banoSEMeta)[[1]] = dem
assay(banoSEMeta[1:3,1:3])
assay(banoSEMeta[1:3,c("NA18498", "NA18501")])

vjcitn/RemoteArray documentation built on May 22, 2019, 12:40 p.m.