pancan_SE {restfulSE}R Documentation

illustrate DelayedArray assay from BigQuery backend in SummarizedExperiment

Description

illustrate DelayedArray assay from BigQuery backend in SummarizedExperiment

Usage

pancan_SE(bqcon, colDataTableName = "clinical_PANCAN_patient_with_followup",
  colDSubjectIdName = "bcr_patient_barcode", colDFilterField = "acronym",
  colDFilterValue = "BRCA",
  assayDataTableName = "pancanMiRs_EBadjOnProtocolPlatformWithoutRepsWithUnCorrectMiRs_08_04_16_annot",
  assayFeatureName = "ID", subjectIDName = "ParticipantBarcode",
  tumorFieldName = "Study", tumorFieldValue = "BRCA",
  assayValueFieldName = "miRNAexpr")

Arguments

bqcon

a BigQueryConnection instance

colDataTableName

character(1) defaulting to "clinical_PANCAN_patient_with_followup"

colDSubjectIdName

character(1) defaulting to "bcr_patient_barcode"

colDFilterField

character(1) defaulting to "acronym"

colDFilterValue

character(1) defaulting to "BRCA"

assayDataTableName

character(1) defaulting to "pancanMiRs_EBadjOnProtocolPlatformWithoutRepsWithUnCorrectMiRs_08_04_16_annot"

assayFeatureName

character(1) defaulting to "ID"

subjectIDName

character(1) defaulting to "ParticipantBarcode"

tumorFieldName

character(1) defaulting to "Study"

tumorFieldValue

character(1) defaulting to "BRCA"

assayValueFieldName

character(1) defaulting to "miRNAexpr"

Value

an instance of SummarizedExperiment

Note

The parameters need different assignments for different tables. Field names are not standardized across tables.

Examples

if (interactive() & requireNamespace("DBI") & 
   requireNamespace("bigrquery")) {
  pancan_BQ_loc = function (dataset="Annotated", 
                billing=Sys.getenv("CGC_BILLING")) 
  {
      con <- DBI::dbConnect(bigrquery::dbi_driver(), 
         project = "pancancer-atlas",         
         dataset = dataset, billing = billing)
      con     
  }
  bqcon = try(pancan_BQ_loc()) # needs CGC_BILLING in environment
  if (!inherits(bqcon, "try-error"))
     pancan_SE(bqcon)
}
[Package restfulSE version 1.2.3 Index]