RESTfulSummarizedExperiment: Construct RESTfulSummarizedExperiment

In restfulSE: Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface

Description

Construct RESTfulSummarizedExperiment

hidden constructor

Usage

RESTfulSummarizedExperiment(se, source)

.RESTfulSummarizedExperiment(se, source)

## S4 method for signature 'RESTfulSummarizedExperiment,missing'
assay(x, i, withDimnames = TRUE, ...)

Arguments

se	SummarizedExperiment instance, assay component can be empty SimpleList
source	instance of H5S_dataset
x	instance of RESTfulSummarizedExperiment
i	not used
...	not used

Value

instance of RESTfulSummarizedExperiment

matrix

Note

RESTfulSummarizedExperiment contains a global dimnames list generated at creation. It is possible that standard operations on a SummarizedExperiment will engender dimnames components that differ from the initial global dimnames, principally through uniqification (adding suffixes when dimname elements are repeated). When this is detected, assay() will fail with a complaint about length(setdiff(*names(x), x@globalDimnames[[...]])).

Examples

require("rhdf5client")
hsds = H5S_source(serverURL=URL_hsds())
hsdsCon = setPath(hsds,"/home/reshg/bano_meQTLex.h5")
fetchDatasets(hsdsCon)
banoh5 = H5S_dataset2(hsdsCon,"d-435d7ad4-9f13-11e8-92c2-0242ac120021")
ehub = ExperimentHub::ExperimentHub()
myfiles <- AnnotationHub::query(ehub , "restfulSEData")
myfiles[["EH551"]] -> banoSEMeta
rr = RESTfulSummarizedExperiment(banoSEMeta, banoh5)
rr
rr2 = rr[1:4, 1:5] # just modify metadata
rr2
assay(rr2) # extract data

restfulSE documentation built on Nov. 8, 2020, 8:01 p.m.