get_TCGA_project_MAF: Get MAF data from TCGA cohort

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

Get MAF data from TCGA cohort

Description

This convenience function queries the Genomic Data Commons API to get MAF data generated with the Aliquot Ensemble Somatic Variant Merging and Masking workflow for the specified project, and writes an MAF file. The API always provides data from the latest data release. This function might work with non-TCGA MAF data hosted on GDC (e.g., TARGET and GENIE-MSK), but it hasn't been tested and users should proceed with caution.

Usage

get_TCGA_project_MAF(
  project = NULL,
  filename = NULL,
  test_run = FALSE,
  exclude_TCGA_nonprimary = TRUE
)

Arguments

project	TCGA project name (e.g., "TCGA-BRCA").
filename	Output filename where MAF data should be saved. Must end in '.maf' (plaintext) or '.maf.gz' (gzip compressed).
test_run	Default FALSE. When TRUE, gets MAF data for a few samples instead of the whole cohort.
exclude_TCGA_nonprimary	Default TRUE. For TCGA projects, exclude samples not associated with a patient's initial primary tumor. (In many TCGA projects, a small handful of patients have metastatic, recurrent, or additional primary samples.)

Details

TCGA cohort MAFs will be structured as downloaded, with a Unique_Patient_Identifier column generated from the first 12 characters of Tumor_Sample_Barcode. When passed to preload_maf() or load_maf(), this column will supersede Tumor_Sample_Barcode. In the handful of patients with multiple Tumor_Sample_Barcodes (essentially replicated sequencing, with very high variant overlap), these functions will effectively take the union of these samples for each patient. Relatedly, the small number of TCGA non-primary tumor samples should not be handled this way (and such samples are by default removed by this function).

Temporary aliquot MAF files downloaded by this function are deleted after they are read.

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.