BQSummarizedExperiment: Define a class to use BigQuery data through...

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

Description

Define a class to use BigQuery data through SummarizedExperiment interface

Slots

rowQref

a BigQueryConnection wrapped in tbl_dbi that holds rowData for the SummarizedExperiment instance

colQref

a BigQueryConnection wrapped in tbl_dbi that holds colData for the SummarizedExperiment instance

rowkey

character(1) name of a field in the table referenced by rowQref to be used as key for features

colkey

character(1) name of a field in the table referenced by colQref to use as key for samples

assayvbl

character(1) name to be used to select table providing assay content

Note

This is an experimental structure to probe the concept that one can use a SummarizedExperiment object to interact with BigQuery data, particularly TCGA data. The slots rowQref and colQref are expected to be BigQuery connections which supply information on features and samples respectively, in a way that is consistent with the assay representation. See seByTumor for illustration.

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