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

View source: R/pancan.R

tumNorSetR Documentation

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.