BQ3_Source: construct a BigQuery resource interface

In restfulSE: Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment 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
}

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