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]