XenaDownload: Download Datasets from UCSC Xena Hubs

In UCSCXenaTools: Download and Explore Datasets from UCSC Xena Data Hubs

Download Datasets from UCSC Xena Hubs

Description

Avaliable datasets list: https://xenabrowser.net/datapages/

Usage

XenaDownload(
  xquery,
  destdir = tempdir(),
  download_probeMap = FALSE,
  trans_slash = FALSE,
  force = FALSE,
  max_try = 3L,
  ...
)

Arguments

xquery	a tibble object generated by XenaQuery function.
destdir	specify a location to store download data. Default is system temp directory.
download_probeMap	if TRUE, also download ProbeMap data, which used for id mapping.
trans_slash	logical, default is FALSE. If TRUE, transform slash '/' in dataset id to '__'. This option is for backwards compatibility.
force	logical. if TRUE, force to download data no matter whether files exist. Default is FALSE.
max_try	time limit to try downloading the data.
...	other argument to download.file function

Value

a tibble

Author(s)

Shixiang Wang [e-mail]

Examples

## Not run: 
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
xe_query = XenaQuery(xe)
xe_download = XenaDownload(xe_query)

## End(Not run)

UCSCXenaTools documentation built on June 20, 2022, 9:05 a.m.