downloadTCGA: Easily Download TCGA Data by Several Options

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/simplify.R

Description

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

1
2
3
4
5
6
7
8
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

Details

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

Value

same as XenaDownload() function result.

Author(s)

Shixiang Wang [email protected]

See Also

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

Examples

1
2
3
4
5
6
7
## Not run: 
# download RNASeq data (use UVM as example)
downloadTCGA(project = "UVM",
                 data_type = "Gene Expression RNASeq",
                 file_type = "IlluminaHiSeq RNASeqV2")

## End(Not run)

ShixiangWang/UCSCXenaTools documentation built on March 25, 2020, 11:09 p.m.