BQ3_Source: construct a BigQuery resource interface

View source: R/BQ3_Array.R

BQ3_SourceR Documentation

construct a BigQuery resource interface

Description

construct a BigQuery resource interface

Usage

BQ3_Source(
  bqconn,
  tblnm = "RNAseq_Gene_Expression",
  rowkeyfield = "Ensembl_gene_id",
  colkeyfield = "case_barcode",
  filtervbl = "project_short_name",
  filterval = "TCGA-GBM",
  assayvbl = "HTSeq__Counts",
  assaysampletype = "TP",
  maxnrec = Inf
)

Arguments

bqconn

instance of BigQueryConnection from bigrquery

tblnm

character(1) table name known to bqconn

rowkeyfield

character(1) field in the table that will generate rownames for matrices derived from table

colkeyfield

character(1) field in the table that will generate colnames for matrices derived from table

filtervbl

character(1) field in the table that will be used to filter out a group of records, for example, all records pertaining to a given tumor in TCGA

filterval

character(1) value in the range of filtervbl to identify records to retain –

assayvbl

character(1) field with assay quantifications

assaysampletype

character(1) value for filtering pancancer-atlas assays, which include normals and other sample types, defaulting to "TP"; ignored if project element of bqconn is not 'pancancer-atlas'

maxnrec

numeric(1) defaults to Inf: number of records to convert with as.data.frame

Value

instance of BQ3_Source

Note

Tailored to ISB-CGC projects 'isb-cgc' and 'pancancer-atlas'.

Examples

if (interactive()) {
 con = cgcConn("TCGA_hg38_data_v0")
 lungConn = BQ3_Source(con, filterval="TCGA-LUAD")
 lungConn
}

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