UCSCXenaTools (version 0.2.4)

XenaHub: Generate a XenaHub Object

Description

Major function of UCSCXenatools. 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("UCSC_Public", "TCGA", "GDC",
  "ICGC", "Toil", "PanCancer", "Treehouse"))

Arguments

hosts

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

cohorts

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

datasets

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

hostName

one to seven of c("UCSC_Public", "TCGA", "GDC", "ICGC", "Toil", "PanCancer", "Treehouse"). This is a 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 = "TCGA")
xe
hosts(xe)     # get hosts
cohorts(xe)   # get cohorts
datasets(xe)  # get datasets
samples(xe)   # get samples
# }