seByTumor_2016: Given a BigQueryConnection to the 2016 ISB TCGA bigtables,...

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

Given a BigQueryConnection to the 2016 ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData

Description

Given a BigQueryConnection to the 2016 ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData

Usage

seByTumor_2016(
  tumorCode = "LUAD",
  assayTblName = "mRNA_UNC_HiSeq_RSEM",
  rdColsToKeep = c("original_gene_symbol", "HGNC_gene_symbol", "gene_id", "Study"),
  bqConn
)

Arguments

tumorCode	one of the concise TCGA codes in a character string – not checked, defaults to "LUAD", lung adenocarcinoma
assayTblName	the name of the assay whose annotation will be used as rowData
rdColsToKeep	columns of assay table to use in rowData component
bqConn	instance of BigQueryConnection from bigrquery

Value

SummarizedExperiment instance, with BigQuery reference as assay

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