assay-BQSummarizedExperiment-missing-method: extract assay data

Description Usage Arguments Value Note

Description

extract assay data

Usage

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

Arguments

x

BQSummarizedExperiment instance

i

index for retrieval, ignored at present

...

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.


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