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

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Documentation for package ‘restfulSE’ version 1.12.0

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.RESTfulSummarizedExperiment Construct RESTfulSummarizedExperiment
assay Construct RESTfulSummarizedExperiment
assay-method Construct RESTfulSummarizedExperiment
assay-method extract assay data
assayNames Placeholder for assay name extractor for a BQSummarizedExperiment instance.
assayNames-method HDF5Server-based assay for SummarizedExperiment
assayNames-method Placeholder for assay name extractor for a BQSummarizedExperiment instance.
assays-method Assays access for RESTfulSummarizedExperiment
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 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.
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"
dim-method dim derived from saved dimnames
dim-method dim derived from saved dimnames
dim-method Dimension access for RESTfulSummarizedExperiment
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
RESTfulSummarizedExperiment Construct RESTfulSummarizedExperiment
RESTfulSummarizedExperiment-class HDF5Server-based assay for SummarizedExperiment
RESTfulSummarizedExperiment-method Construct RESTfulSummarizedExperiment
se1.3M Convenience functions using HSDS server to extract tenx neurons full or subset data
se100k 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.
[-method HDF5Server-based assay for SummarizedExperiment