pancan_SE: illustrate DelayedArray assay from BigQuery backend in...

Description Usage Arguments Value Note Examples

View source: R/pancan_SE.R

Description

illustrate DelayedArray assay from BigQuery backend in SummarizedExperiment

Usage

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

Arguments

bqcon

a BigQueryConnection instance

colDataTableName

character(1) defaulting to "clinical_PANCAN_patient_with_followup"

clinVars

character() vector of variables to be retained from the table named by 'colDataTableName', defaults to vector returned by clinVars()

colDSubjectIdName

character(1) defaulting to "bcr_patient_barcode"

colDFilterField

character(1) defaulting to "acronym"

colDFilterValue

character(1) defaulting to "BRCA"; a vector may be used, in which case multiple tumor types will be represented – must agree with tumorFieldValue, as clinical and assay data are collected separately

assayDataTableName

character(1) defaulting to "pancanMiRs_EBadjOnProtocolPlatformWithoutRepsWithUnCorrectMiRs_08_04_16_annot"

assayFeatureName

character(1) defaulting to "ID"

assaySampleTypeCode

character(1) defaulting to "TP"

subjectIDName

character(1) defaulting to "ParticipantBarcode"

tumorFieldName

character(1) defaulting to "Study"

tumorFieldValue

character() defaulting to "BRCA"; a vector may be used in which case multiple tumor types will be represented – must agree with colDFilterValue

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 as of August 2018. AUTHENTICATION CONCERNS: You must have a valid BigQuery project identifier in the environment variable CGC_BILLING, or pass such as 'billing' when using DBI::dbConnect(bigquery::bigrquery(), ...). To get such a project identifier, you need to have a Google identity and you must have created a BigQuery project with that identity. Notes at https://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/progapi/bigqueryGUI/WalkthroughOfGoogleBigQuery.html provide details. Another approach that can be used involves the Google Cloud SDK. Assuming you have a Google identity and have installed a recent SDK instance, you can use (in the shell) gcloud auth login to pick the identity that has a project with id PROJECT_ID. Use that project id as the billing code for bigrquery dbConnect, or set CGC_BILLING in the environment to evaluate to that project id.

Examples

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if (interactive() & requireNamespace("DBI") & 
   requireNamespace("bigrquery")) {
     billco = Sys.getenv("CGC_BILLING")
     if (nchar(billco)==0) 
          stop("need CGC_BILLING set to your BigQuery project ID, see note in ?pancan_SE")
     bqcon = DBI::dbConnect(bigrquery::bigquery(), project = "pancancer-atlas", 
           dataset = "Annotated", billing = billco)
     brca_mirSE = pancan_SE(bqcon)
     brca_mirSE
     }

restfulSE documentation built on Nov. 8, 2020, 8:01 p.m.