assay-BQSummarizedExperiment-missing-method: extract assay data

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

extract assay data

Description

extract assay data

Usage

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

Arguments

x	BQSummarizedExperiment instance
i	index for retrieval, ignored at present
withDimnames	logical(1)
...	not used

Value

matrix

Note

Very experimental approach to retrieving numerical data given a SummarizedExperiment 'shell'. We need more checking of consistency between assay and clinical data before creating the shell. We use dcast to transform query result to a matrix, and some 'individuals' may have multiple contributions ... we use fun.aggregate = max and will see warnings until this is cleared up.

vjcitn/restfulSE documentation built on Nov. 1, 2022, 7:33 a.m.