seByTumor {restfulSE} | R Documentation

## Given a BigQueryConnection to the 2017 GDC-oriented ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData

### Description

Given a BigQueryConnection to the 2017 GDC-oriented ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData

### Usage

    seByTumor(tumorCode = "LUAD", assayTblName = "RNAseq_Gene_Expression",
      rdColsToKeep = c("gene_name", "Ensembl_gene_id", "gene_type"),
      bqConnClinical, bqConnAssay, rowkey = "Ensembl_gene_id",
      colkey = "case_barcode", assayvbl = "HTSeq__Counts")

### 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
`bqConnClinical` | instance of BigQueryConnection from bigrquery, for access to clinical metadata – current expectation is that the BigQuery dataset is named "TCGA_bioclin_v0" and has a table called "Clinical"
`bqConnAssay` | instance of BigQueryConnection from bigrquery – current expectation is that the BigQuery dataset is named "TCGA_hg19_data_v0"
`rowkey` | name of a field to be used as key for rows
`colkey` | name of a field to use as key for samples
`assayvbl` | name of field to use for numerical values

### Value

SummarizedExperiment

### Note

This function demonstrates the use of external resources for rowData, colData and assay components of a SummarizedExperiment instance. The intention is that the full complement of activities supported by `SummarizedExperiment-class` are likewise supported through this class, with assay data and sample and feature metadata all external and in BigQuery projects. The `seByTumor` function is provided to generate an example of this approach with minimal user configuration.

### Examples

    if (interactive()) {
     require(bigrquery)
     # be sure that .cgcBilling is set
     code = Sys.getenv("CGC_BILLING")
     if (!(nchar(code)==0)) {
      clinQ = cgcConn(billing=code)
      assayQ = cgcConn( dataset = "TCGA_hg38_data_v0", billing=code )
      myexpShell = seByTumor( bqConnClinical=clinQ,
            bqConnAssay=assayQ)
      print(myexpShell)
      print(nrow(myexpShell) == 60483)
      print(ncol(myexpShell) == 522)
      assay(myexpShell[11:15,1:4]) # some case_barcodes repeat
      }
     }

[Package restfulSE version 1.2.3 Index]