[ea2224]: / man / XenaHub.Rd

Download this file

55 lines (51 with data), 1.7 kB

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/XenaHub-class.R
\name{XenaHub}
\alias{XenaHub}
\title{Generate a XenaHub Object}
\usage{
XenaHub(
hosts = xena_default_hosts(),
cohorts = character(),
datasets = character(),
hostName = c("publicHub", "tcgaHub", "gdcHub", "gdcHubV18", "icgcHub", "toilHub",
"pancanAtlasHub", "treehouseHub", "pcawgHub", "atacseqHub", "singlecellHub",
"kidsfirstHub", "tdiHub")
)
}
\arguments{
\item{hosts}{a character vector specify UCSC Xena hosts, all available hosts can be
found by \code{xena_default_hosts()} function. \code{hostName} is a more recommend option.}
\item{cohorts}{default is empty character vector, all cohorts will be returned.}
\item{datasets}{default is empty character vector, all datasets will be returned.}
\item{hostName}{name of host, available options can be accessed by \code{.xena_hosts}
This is an easier option for user than \code{hosts} option. Note, this option
will overlap \code{hosts}.}
}
\value{
a \link{XenaHub} object
}
\description{
It is used to generate original
\code{XenaHub} object according to hosts, cohorts, datasets or hostName.
If these arguments not specified, all hosts and corresponding datasets
will be returned as a \code{XenaHub} object. All datasets can be found
at \url{https://xenabrowser.net/datapages/}.
}
\examples{
\dontrun{
#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
}
}
\author{
Shixiang Wang \href{mailto:w_shixiang@163.com}{w_shixiang@163.com}
}