GDCdownload: Download GDC data

Description Usage Arguments Value Examples

View source: R/download.R

Description

Uses GDC API or GDC transfer tool to download gdc data The user can use query argument The data from query will be save in a folder: project/data.category

Usage

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GDCdownload(
  query,
  token.file,
  method = "api",
  directory = "GDCdata",
  files.per.chunk = NULL
)

Arguments

query

A query for GDCquery function

token.file

Token file to download controlled data (only for method = "client")

method

Uses the API (POST method) or gdc client tool. Options "api", "client". API is faster, but the data might get corrupted in the download, and it might need to be executed again

directory

Directory/Folder where the data was downloaded. Default: GDCdata

files.per.chunk

This will make the API method only download n (files.per.chunk) files at a time. This may reduce the download problems when the data size is too large. Expected a integer number (example files.per.chunk = 6)

Value

Shows the output from the GDC transfer tools

Examples

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query <- GDCquery(project = "TCGA-ACC",
                 data.category =  "Copy number variation",
                 legacy = TRUE,
                 file.type = "hg19.seg",
                 barcode = c("TCGA-OR-A5LR-01A-11D-A29H-01", "TCGA-OR-A5LJ-10A-01D-A29K-01"))
# data will be saved in  GDCdata/TCGA-ACC/legacy/Copy_number_variation/Copy_number_segmentation
GDCdownload(query, method = "api")
## Not run: 
    # Download clinical data from XML
    query <- GDCquery(project = "TCGA-COAD", data.category = "Clinical")
    GDCdownload(query, files.per.chunk = 200)
    query <- GDCquery(project = "TARGET-AML",
                  data.category = "Transcriptome Profiling",
                  data.type = "miRNA Expression Quantification",
                  workflow.type = "BCGSC miRNA Profiling",
                  barcode = c("TARGET-20-PARUDL-03A-01R","TARGET-20-PASRRB-03A-01R"))
    # data will be saved in:
    # example_data_dir/TARGET-AML/harmonized/Transcriptome_Profiling/miRNA_Expression_Quantification
    GDCdownload(query, method = "client", directory = "example_data_dir")
    acc.gbm <- GDCquery(project =  c("TCGA-ACC","TCGA-GBM"),
                        data.category = "Transcriptome Profiling",
                        data.type = "Gene Expression Quantification",
                        workflow.type = "HTSeq - Counts")
    GDCdownload(acc.gbm, method = "api", directory = "example", files.per.chunk = 50)

## End(Not run)

daniel615212950/TCGAbiolinks documentation built on Dec. 19, 2021, 8:06 p.m.