Download Datasets from UCSC Xena Hubs

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

Shixiang Wang [email protected]

Examples

if (FALSE) {
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
xe_query = XenaQuery(xe)
xe_download = XenaDownload(xe_query)
}