Function reference • UCSCXenaTools

Standard dataset query and download pipeline

Select, query, download and load datasets.

XenaData: Xena Hub Information

XenaScan(): Scan all rows according to user input by a regular expression

XenaGenerate(): Generate and Subset a XenaHub Object from 'XenaData'

XenaFilter(): Filter a XenaHub Object

XenaBrowse(): View Info of Dataset or Cohort at UCSC Xena Website Using Web browser

XenaQuery(): Query URL of Datasets before Downloading

XenaDownload(): Download Datasets from UCSC Xena Hubs

XenaPrepare(): Prepare (Load) Downloaded Datasets to R

Download a subset of dataset

Download a subset of dataset for target analysis.

fetch() fetch_dense_values() fetch_sparse_values() fetch_dataset_samples() fetch_dataset_identifiers() has_probeMap(): Fetch Data from UCSC Xena Hosts

One-click download function

Download datasets by setting options in one function.

downloadTCGA(): Easily Download TCGA Data by Several Options

getTCGAdata(): Get TCGA Common Data Sets by Project ID and Property

availTCGA(): Get or Check TCGA Available ProjectID, DataType and FileType

showTCGA(): Show TCGA data structure by Project ID or ALL

Utility

Useful functions.

XenaDataUpdate(): Get or Update Newest Data Information of UCSC Xena Data Hubs

XenaShiny(): Xena Shiny App

hosts(): Get hosts of XenaHub object

cohorts(): Get cohorts of XenaHub object

datasets(): Get datasets of XenaHub object

samples(): Get Samples of a XenaHub object according to 'by' and 'how' action arguments

fetch() fetch_dense_values() fetch_sparse_values() fetch_dataset_samples() fetch_dataset_identifiers() has_probeMap(): Fetch Data from UCSC Xena Hosts

XenaQueryProbeMap(): Query ProbeMap URL of Datasets

Helpers

Helper functions.

xena_default_hosts(): UCSC Xena Default Hosts

to_snake(): Convert camel case to snake case

Class

Class and related function.

XenaHub-class: Class XenaHub

XenaHub(): Generate a XenaHub Object