UCSCXenaTools (version 1.4.8)

XenaHub: Generate a XenaHub Object

Description

It is used to generate original XenaHub object according to hosts, cohorts, datasets or hostName. If these arguments not specified, all hosts and corresponding datasets will be returned as a XenaHub object. All datasets can be found at https://xenabrowser.net/datapages/.

Usage

XenaHub(
  hosts = xena_default_hosts(),
  cohorts = character(),
  datasets = character(),
  hostName = c("publicHub", "tcgaHub", "gdcHub", "icgcHub", "toilHub",
    "pancanAtlasHub", "treehouseHub", "pcawgHub", "atacseqHub", "singlecellHub",
    "kidsfirstHub")
)

Arguments

hosts

a character vector specify UCSC Xena hosts, all available hosts can be found by xena_default_hosts() function. hostName is a more recommend option.

cohorts

default is empty character vector, all cohorts will be returned.

datasets

default is empty character vector, all datasets will be returned.

hostName

name of host, available options can be accessed by .xena_hosts This is an easier option for user than hosts option. Note, this option will overlap hosts.

Value

a XenaHub object

Examples

# NOT RUN {
#1 query all hosts, cohorts and datasets
xe = XenaHub()
xe
#2 query only TCGA hosts
xe = XenaHub(hostName = "tcgaHub")
xe
hosts(xe)     # get hosts
cohorts(xe)   # get cohorts
datasets(xe)  # get datasets
samples(xe)   # get samples
# }