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Easily Download TCGA Data by Several Options

Source: R/simplify.R
downloadTCGA.Rd

TCGA is a very useful database and here we provide this function to download TCGA (include TCGA Pancan) datasets in human-friendly way. Users who are not familiar with R operation will benefit from this.

Usage

downloadTCGA(
  project = NULL,
  data_type = NULL,
  file_type = NULL,
  destdir = tempdir(),
  force = FALSE,
  ...
)

Arguments

project

default is NULL. Should be one or more of TCGA project id (character vector) provided by Xena. See all available project id, please use availTCGA("ProjectID").

data_type

default is NULL. Should be a character vector specify data type. See all available data types by availTCGA("DataType").

file_type

default is NULL. Should be a character vector specify file type. See all available file types by availTCGA("FileType").

destdir

specify a location to store download data. Default is system temp directory.

force

logical. if TRUE, force to download data no matter whether files exist. Default is FALSE.

...

other argument to download.file function

Value

same as XenaDownload() function result.

Details

All availble information about datasets of TCGA can access vis availTCGA() and check with showTCGA().

See also

XenaQuery(), XenaFilter(), XenaDownload(), XenaPrepare(), availTCGA(), showTCGA()

Author

Shixiang Wang w_shixiang@163.com

Examples

if (FALSE) { # \dontrun{
# download RNASeq data (use UVM as example)
downloadTCGA(project = "UVM",
                 data_type = "Gene Expression RNASeq",
                 file_type = "IlluminaHiSeq RNASeqV2")
} # }