download_gdc: Download data from GDC Data Portal and GDC Legacy Archive

In Facottons/DOAGDC: A Package to Download, Organize and Analyze Genomic Data Commons (GDC) Data

Description

download_gdc is a function designed to download methylation, mutation, clinical data, protein expression, MAGETAB, gene expression, isoform expression, miRNA expression and clinical images data from GDC Data Portal and GDC Legacy Archive.

Usage

download_gdc(
  data_type = "gene",
  tumor,
  data_base = "legacy",
  htseq = "",
  work_dir,
  all_files = FALSE,
  platform = "all"
)

Arguments

data_type	Type of data. It could be "methylation", "mutation", "clinical_supplement", "biospecimen", "gene", or "clinical"(biotab). Only present in "Legacy" database:"protein", "Exon quantification", "miRNA gene quantification", "miRNA isoform quantification", "isoform", and "image". Only present in "GDC" database:"miRNA Expression Quantification", and "Isoform Expression Quantification" (miRNA).
tumor	A character string contaning one of the 33 tumors available in the TCGA project. For instance, the "BRCA" stands for breast cancer.
data_base	A character string specifying "GDC" for GDC Data Portal or "legacy" for GDC Legacy Archive.
htseq	A character string indicating which HTSeq workflow data should be downloaded: "Counts", "FPKM", or "all". The default is "all".
work_dir	A character string specifying the path to work directory.
all_files	A logical value. Set FALSE to avoid the download of not used data to reduce download size, e.g. quantification files. The default is FALSE.
platform	A character string indicating the platform name for methylation, exon quantificaton, miRNA, and mutation data. For mutation and exon quantificaton data:"Illumina GA", "Illumina HiSeq" or "all". For methylation data"Illumina Human Methylation 450", "Illumina Human Methylation 27" or "all". For miRNA data:"Illumina GA", "Illumina HiSeq", "H-miRNA_8x15K" (for GBM tumor), "H-miRNA_8x15Kv2" (for OV tumor), or "all". The default for all data_type cited is "all" (when downloading data).

Value

the files download are stored inside the determined folders in the user machine.

Examples

library(DOAGDC)

# Downloading gene expression data from GDC Legacy Archive
download_gdc("gene", "CHOL", "legacy", work_dir = "~/Desktop")

Facottons/DOAGDC documentation built on April 7, 2020, 3:17 a.m.