RESTfulSummarizedExperiment {restfulSE} | R Documentation |
Construct RESTfulSummarizedExperiment
hidden constructor
RESTfulSummarizedExperiment(se, source) .RESTfulSummarizedExperiment(se, source) ## S4 method for signature 'RESTfulSummarizedExperiment,missing' assay(x, i, ...)
se |
SummarizedExperiment instance, assay component can be empty SimpleList |
source |
instance of H5S_dataset |
x |
instance of RESTfulSummarizedExperiment |
i |
not used |
... |
not used |
instance of RESTfulSummarizedExperiment
matrix
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[[...]])).
require("rhdf5client") bigec2 = H5S_source(serverURL="http://h5s.channingremotedata.org:5000") banoh5 = bigec2[["assays"]] # banovichSE 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