tumNorSet: create list with SEs for tumor and normal for a tumor/assay...

In vjcitn/BiocOncoTK: Bioconductor components for general cancer genomics

create list with SEs for tumor and normal for a tumor/assay pairing

Description

create list with SEs for tumor and normal for a tumor/assay pairing

Usage

tumNorSet(
  bq,
  code = "PRAD",
  assayDataTableName = pancan_longname("rnaseq"),
  assayValueFieldName = "normalized_count",
  assayFeatureName = "Entrez"
)

Arguments

bq	a BigQuery connection
code	character(1) a TCGA tumor code, defaults to "PRAD" for prostate tumor
assayDataTableName	character(1) name of table in BigQuery
assayValueFieldName	character(1) field from which assay quantifications are retrieved
assayFeatureName	character(1) field from which assay feature names are retrieved

Examples

if (interactive()) {
 bqcon = try(pancan_BQ())
 if (!inherits(bqcon, "try-error")) {
   tn = tumNorSet(bqcon)
   tn
 }
}

vjcitn/BiocOncoTK documentation built on Feb. 14, 2023, 11:56 p.m.