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

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Documentation for package ‘restfulSE’ version 1.22.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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assay-method	extract assay data
assayNames	Placeholder for assay name extractor for a BQSummarizedExperiment instance.
assayNames-method	Placeholder for assay name extractor for a BQSummarizedExperiment instance.
basic_clinvars	provide a collection of basic clinical variables to limit size of clinical data return
BQ3_Array	create BQ3_Array instance given url (filepath) and entity (host) name
BQ3_Array-class	extension of DelayedArray for BigQuery content
BQ3_ArraySeed-class	BQ3_Array for BigQuery matrix content
BQ3_Matrix-class	extension of DelayedMatrix for HDF Server content
BQ3_Source	construct a BigQuery resource interface
BQ3_Source-class	a class for BigQuery tables with keys and filters baked in
bqConn	generate a connection to BigQuery for specific dataset
BQM_Array	create BQM_Array instance given url (filepath) and entity (host) name
BQM_Array-class	extension of DelayedArray for BigQuery content
BQM_ArraySeed-class	BQM_Array for BigQuery matrix content
BQM_Matrix-class	extension of DelayedMatrix for HDF Server content
BQM_Source	construct a BigQuery resource interface, for a matrix-like table with one column devoted to row identification (rowkeyfield) and all other columns assumed numeric
BQM_Source-class	Represent information about a BigQuery resource with a 'triple' database schema. This is targeting the isb-cgc TCGA layout. BigQuery Records are regarded as triples, within major groups defined by filtervbl. Triples have content subject - gene - value, to be pivoted to genes(rows) x subjects(columns) with values as entries.
BQSummarizedExperiment-class	Define a class to use BigQuery data through SummarizedExperiment interface
cgcConn	Simplify connection to a BigQuery dataset for the project "isb-cgc"
DelayedArray-method	constructor
dim-method	dim derived from saved dimnames
dim-method	dim derived from saved dimnames
dimnames-method	dimnames are saved in the BQ3_ArraySeed
dimnames-method	dimnames are saved in the BQM_ArraySeed
goPatt	Create a data.frame with ENSEMBL and SYMBOL identifiers associated with a GO TERM specified by a regular expression in 'termPattern'
gtexTiss	Convenience function for access to gene-level GTEx tissues, as quantified in recount
isbCgcDatasets	Access the dataset names in the "isb-cgc" project
isbCgcTables	List the tables in a selected dataset
newDA	DelayedArray bridge
pancan_SE	illustrate DelayedArray assay from BigQuery backend in SummarizedExperiment
se1.3M	Convenience functions using HSDS server to extract tenx neurons full or subset data
seByTumor	Given a BigQueryConnection to the 2017 GDC-oriented ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData
seByTumor_2016	Given a BigQueryConnection to the 2016 ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData
tasicCortex	A set of mouse cortex marker genes.