get_plates: use curatedTCGAData request to acquire plate codes for...

In vjcitn/BiocOncoTK: Bioconductor components for general cancer genomics

use curatedTCGAData request to acquire plate codes for samples

Description

use curatedTCGAData request to acquire plate codes for samples

Usage

get_plates(
  tumcode = "BLCA",
  assay = "RNASeq2GeneNorm",
  samptypes = c("01", "02", "03", "04", "06", "09", "40")
)

Arguments

tumcode	a TCGA tumor code, usually 3 or for characters
assay	a curatedTCGAData assay code, run curatedTCGAData() to see a message with available options
samptypes	a character vector with codes as defined at https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes

Value

a data.frame with a row for each TCGA contribution for the selected tumor type and assay type

Examples

if (interactive()) {
 plts_blca_rnaseq = get_plates()
 dim(plts_blca_rnaseq)
 head(plts_blca_rnaseq)
}

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