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**UCSCXenaTools** is an R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
Public omics data from UCSC Xena are supported through [**multiple turn-key Xena Hubs**](https://xenabrowser.net/datapages/), which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
@@ -194,16 +121,7 @@ df_todo
Query and download.
-```{r, eval=FALSE}
-XenaQuery(df_todo) %>%
- XenaDownload() -> xe_download
-```
-
-**For researchers in China, now Hiplot team has deployed several Xena mirror sites (`https://xena.hiplot.com.cn/`) at Shanghai. You can set an option `options(use_hiplot = TRUE)` before querying data step to speed up both data querying and downloading.**
-
```{r}
-options(use_hiplot = TRUE)
-
XenaQuery(df_todo) %>%
XenaDownload() -> xe_download
```
diff --git a/README.md b/README.md
index c6f9663..22d5a83 100644
--- a/README.md
+++ b/README.md
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+# UCSCXenaTools
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**UCSCXenaTools** is an R package for accessing genomics data from UCSC
Xena platform, from cancer multi-omics to single-cell RNA-seq. Public
@@ -92,17 +26,17 @@ filtered, explored and downloaded.
**Who is the target audience and what are scientific applications of
this package?**
-- Target Audience: cancer and clinical researchers, bioinformaticians
-- Applications: genomic and clinical analyses
+- Target Audience: cancer and clinical researchers, bioinformaticians
+- Applications: genomic and clinical analyses
## Table of Contents
-- [Installation](#installation)
-- [Data Hub List](#data-hub-list)
-- [Basic usage](#basic-usage)
-- [Citation](#citation)
-- [How to contribute](#how-to-contribute)
-- [Acknowledgment](#acknowledgment)
+- [Installation](#installation)
+- [Data Hub List](#data-hub-list)
+- [Basic usage](#basic-usage)
+- [Citation](#citation)
+- [How to contribute](#how-to-contribute)
+- [Acknowledgment](#acknowledgment)
## Installation
@@ -133,18 +67,18 @@ All datasets are available at Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>
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-An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
-Copyright (C) 2019 Shixiang Wang
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.Also add information on how to contact you by electronic and paper mail.
-If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
-UCSCXenaTools Copyright (C) 2019 Shixiang Wang
-This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
-This is free software, and you are welcome to redistribute it
-under certain conditions; type 'show c' for details.The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.
-The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.
-vignettes/USCSXenaTools.Rmd
- USCSXenaTools.RmdUCSCXenaTools is an R package for accessing genomics -data from UCSC Xena platform, from cancer multi-omics to single-cell -RNA-seq. Public omics data from UCSC Xena are supported through multiple turn-key Xena -Hubs, which are a collection of UCSC-hosted public -databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases -are normalized so they can be combined, linked, filtered, explored and -downloaded.
-Who is the target audience and what are scientific -applications of this package?
-Install stable release from CRAN with:
-
-install.packages("UCSCXenaTools")You can also install devel version of UCSCXenaTools -from github with:
-
-# install.packages("remotes")
-remotes::install_github("ropensci/UCSCXenaTools")If you want to build vignette in local, please add two options:
-
-remotes::install_github("ropensci/UCSCXenaTools", build_vignettes = TRUE, dependencies = TRUE)The minimum versions to run the vignette is 1.2.4. GitHub Issue
-is a place for discussing any problem.
All datasets are available at https://xenabrowser.net/datapages/.
-Currently, UCSCXenaTools supports the following data -hubs of UCSC Xena.
-Users can update dataset list from the newest version of UCSC Xena by
-hand with XenaDataUpdate() function, followed by restarting
-R and library(UCSCXenaTools).
If any url of data hub is changed or a new data hub is online, please -remind me by emailing to w_shixiang@163.com or opening an issue -on GitHub.
-Download UCSC Xena datasets and load them into R by
-UCSCXenaTools is a workflow with generate,
-filter, query, download and
-prepare 5 steps, which are implemented as
-XenaGenerate, XenaFilter,
-XenaQuery, XenaDownload and
-XenaPrepare functions, respectively. They are very clear
-and easy to use and combine with other packages like
-dplyr.
To show the basic usage of UCSCXenaTools, we will -download clinical data of LUNG, LUAD, LUSC from TCGA (hg19 version) data -hub.
-UCSCXenaTools uses a data.frame object
-(built in package) XenaData to generate an instance of
-XenaHub class, which records information of all datasets of
-UCSC Xena Data Hubs.
You can load XenaData after loading
-UCSCXenaTools into R.
-library(UCSCXenaTools)
-#> =========================================================================================
-#> UCSCXenaTools version 1.4.8
-#> Project URL: https://github.com/ropensci/UCSCXenaTools
-#> Usages: https://cran.r-project.org/web/packages/UCSCXenaTools/vignettes/USCSXenaTools.html
-#>
-#> If you use it in published research, please cite:
-#> Wang et al., (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data
-#> from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
-#> Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627
-#> =========================================================================================
-#> --Enjoy it--
-data(XenaData)
-
-head(XenaData)
-#> # A tibble: 6 × 17
-#> XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label
-#> <chr> <chr> <chr> <chr> <int> <chr> <chr>
-#> 1 https://… publicHub Breast Can… ucsfNeve_pu… 51 gene expre… Neve…
-#> 2 https://… publicHub Breast Can… ucsfNeve_pu… 57 phenotype Phen…
-#> 3 https://… publicHub Glioma (Ko… kotliarov20… 194 copy number Kotl…
-#> 4 https://… publicHub Glioma (Ko… kotliarov20… 194 phenotype Phen…
-#> 5 https://… publicHub Lung Cance… weir2007_pu… 383 copy number CGH
-#> 6 https://… publicHub Lung Cance… weir2007_pu… 383 phenotype Phen…
-#> # … with 10 more variables: Type <chr>, AnatomicalOrigin <chr>,
-#> # SampleType <chr>, Tags <chr>, ProbeMap <chr>, LongTitle <chr>,
-#> # Citation <chr>, Version <chr>, Unit <chr>, Platform <chr>Select datasets.
-
-# The options in XenaFilter function support Regular Expression
-XenaGenerate(subset = XenaHostNames=="tcgaHub") %>%
- XenaFilter(filterDatasets = "clinical") %>%
- XenaFilter(filterDatasets = "LUAD|LUSC|LUNG") -> df_todo
-
-df_todo
-#> class: XenaHub
-#> hosts():
-#> https://tcga.xenahubs.net
-#> cohorts() (3 total):
-#> TCGA Lung Cancer (LUNG)
-#> TCGA Lung Adenocarcinoma (LUAD)
-#> TCGA Lung Squamous Cell Carcinoma (LUSC)
-#> datasets() (3 total):
-#> TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
-#> TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
-#> TCGA.LUSC.sampleMap/LUSC_clinicalMatrixSometimes we only know some keywords, XenaScan() can be
-used to scan all rows to detect if the keywords exist in
-XenaData.
-x1 = XenaScan(pattern = 'Blood')
-x2 = XenaScan(pattern = 'LUNG', ignore.case = FALSE)
-
-x1 %>%
- XenaGenerate()
-#> class: XenaHub
-#> hosts():
-#> https://ucscpublic.xenahubs.net
-#> https://tcga.xenahubs.net
-#> cohorts() (6 total):
-#> Connectivity Map
-#> TARGET Acute Lymphoblastic Leukemia
-#> Pediatric tumor (Khan)
-#> Acute lymphoblastic leukemia (Mullighan 2008)
-#> TCGA Pan-Cancer (PANCAN)
-#> TCGA Acute Myeloid Leukemia (LAML)
-#> datasets() (28 total):
-#> cmap/rankMatrix_reverse
-#> TARGET_ALL/TARGETcnv_genomicMatrix
-#> TARGET_ALL/TARGETexp_genomicMatrix
-#> ...
-#> TCGA.LAML.sampleMap/mutation_wustl
-#> TCGA.LAML.sampleMap/mutation_wustl_gene
-x2 %>%
- XenaGenerate()
-#> class: XenaHub
-#> hosts():
-#> https://tcga.xenahubs.net
-#> cohorts() (1 total):
-#> TCGA Lung Cancer (LUNG)
-#> datasets() (15 total):
-#> TCGA.LUNG.sampleMap/HumanMethylation27
-#> TCGA.LUNG.sampleMap/HumanMethylation450
-#> TCGA.LUNG.sampleMap/Gistic2_CopyNumber_Gistic2_all_data_by_genes
-#> ...
-#> mc3/LUNG_mc3.txt
-#> mc3_gene_level/LUNG_mc3_gene_level.txtQuery and download.
-
-XenaQuery(df_todo) %>%
- XenaDownload() -> xe_downloadFor researchers in China, now Hiplot team has deployed
-several Xena mirror sites (https://xena.hiplot.com.cn/) at
-Shanghai. You can set an option options(use_hiplot = TRUE)
-before querying data step to speed up both data querying and
-downloading.
-options(use_hiplot = TRUE)
-
-XenaQuery(df_todo) %>%
- XenaDownload() -> xe_download
-#> Use hiplot server (China) for mirrored data hubs (set 'options(use_hiplot = FALSE)' to disable it)
-#> This will check url status, please be patient.
-#> All downloaded files will under directory /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh80000gn/T//RtmpwtHWjn.
-#> The 'trans_slash' option is FALSE, keep same directory structure as Xena.
-#> Creating directories for datasets...
-#> Downloading TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
-#> Downloading TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
-#> Downloading TCGA.LUSC.sampleMap/LUSC_clinicalMatrixPrepare data into R for analysis.
-
-cli = XenaPrepare(xe_download)
-class(cli)
-#> [1] "list"
-names(cli)
-#> [1] "LUNG_clinicalMatrix" "LUAD_clinicalMatrix" "LUSC_clinicalMatrix"Create two XenaHub objects:
-to_browse - a XenaHub object containing a cohort and a
-dataset.to_browse2 - a XenaHub object containing 2 cohorts and
-2 datasets.
-XenaGenerate(subset = XenaHostNames=="tcgaHub") %>%
- XenaFilter(filterDatasets = "clinical") %>%
- XenaFilter(filterDatasets = "LUAD") -> to_browse
-
-to_browse
-#> class: XenaHub
-#> hosts():
-#> https://tcga.xenahubs.net
-#> cohorts() (1 total):
-#> TCGA Lung Adenocarcinoma (LUAD)
-#> datasets() (1 total):
-#> TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
-
-XenaGenerate(subset = XenaHostNames=="tcgaHub") %>%
- XenaFilter(filterDatasets = "clinical") %>%
- XenaFilter(filterDatasets = "LUAD|LUSC") -> to_browse2
-
-to_browse2
-#> class: XenaHub
-#> hosts():
-#> https://tcga.xenahubs.net
-#> cohorts() (2 total):
-#> TCGA Lung Adenocarcinoma (LUAD)
-#> TCGA Lung Squamous Cell Carcinoma (LUSC)
-#> datasets() (2 total):
-#> TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
-#> TCGA.LUSC.sampleMap/LUSC_clinicalMatrixXenaBrowse() function can be used to browse
-dataset/cohort links using your default web browser. At default, this
-function limits one dataset/cohort for preventing user to open too many
-links at once.
-# This will open you web browser
-XenaBrowse(to_browse)
-
-XenaBrowse(to_browse, type = "cohort")
-# This will throw error
-XenaBrowse(to_browse2)
-#> Error in XenaBrowse(to_browse2): This function limite 1 dataset to browse.
-#> Set multiple to TRUE if you want to browse multiple links.
-
-XenaBrowse(to_browse2, type = "cohort")
-#> Error in XenaBrowse(to_browse2, type = "cohort"): This function limite 1 cohort to browse.
-#> Set multiple to TRUE if you want to browse multiple links.When you make sure you want to open multiple links, you can set
-multiple option to TRUE.
-XenaBrowse(to_browse2, multiple = TRUE)
-XenaBrowse(to_browse2, type = "cohort", multiple = TRUE)The core functionality has been described above. I write more usages -about this package in my website but not here because sometimes package -check will fail due to internet problem.
-Read Obtain -RNAseq Values for a Specific Gene in Xena Database to see how to get -values for single gene. A use case for survival analysis based on single -gene expression has been published on rOpenSci, please read UCSCXenaTools: -Retrieve Gene Expression and Clinical Information from UCSC Xena for -Survival Analysis.
-Thanks to the UCSC Xena team, the new feature ‘resume from
-breakpoint’ is added and can be done by XenaDownload()
-with the method and extra flags specified.
Of note, the corresponding wget or curl
-command must be installed by your OS and can be found by R.
The folliwng code gives a test example, the data can be viewed on web -page.
-
-library(UCSCXenaTools)
-xe = XenaGenerate(subset = XenaDatasets == "TcgaTargetGtex_expected_count")
-xe
-xq = XenaQuery(xe)
-# You cannot resume from breakpoint in default mode
-XenaDownload(xq, destdir = "~/test/", force = TRUE)
-# You can do it with 'curl' command
-XenaDownload(xq, destdir = "~/test/", method = "curl", extra = "-C -", force = TRUE)
-# You can do it with 'wget' command
-XenaDownload(xq, destdir = "~/test/", method = "wget", extra = "-c", force = TRUE)Cite me by the following paper.
-Wang et al., (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data
- from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
- Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627
-
-# For BibTex
-
-@article{Wang2019UCSCXenaTools,
- journal = {Journal of Open Source Software},
- doi = {10.21105/joss.01627},
- issn = {2475-9066},
- number = {40},
- publisher = {The Open Journal},
- title = {The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq},
- url = {http://dx.doi.org/10.21105/joss.01627},
- volume = {4},
- author = {Wang, Shixiang and Liu, Xuesong},
- pages = {1627},
- date = {2019-08-05},
- year = {2019},
- month = {8},
- day = {5},
-}Cite UCSC Xena by the following paper.
-Goldman, Mary, et al. "The UCSC Xena Platform for cancer genomics data
- visualization and interpretation." BioRxiv (2019): 326470.This package is based on XenaR, thanks Martin Morgan for his work.
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UCSCXenaTools is an R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. Public omics data from UCSC Xena are supported through multiple turn-key Xena Hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
-Who is the target audience and what are scientific applications of this package?
-Install stable release from CRAN with:
-
-install.packages("UCSCXenaTools")You can also install devel version of UCSCXenaTools from github with:
-
-# install.packages("remotes")
-remotes::install_github("ropensci/UCSCXenaTools")If you want to build vignette in local, please add two options:
-
-remotes::install_github("ropensci/UCSCXenaTools", build_vignettes = TRUE, dependencies = TRUE)All datasets are available at https://xenabrowser.net/datapages/.
-Currently, UCSCXenaTools supports the following data hubs of UCSC Xena.
-Users can update dataset list from the newest version of UCSC Xena by hand with XenaDataUpdate() function, followed by restarting R and library(UCSCXenaTools).
If any url of data hub is changed or a new data hub is online, please remind me by emailing to w_shixiang@163.com or opening an issue on GitHub.
-Download UCSC Xena datasets and load them into R by UCSCXenaTools is a workflow with generate, filter, query, download and prepare 5 steps, which are implemented as XenaGenerate, XenaFilter, XenaQuery, XenaDownload and XenaPrepare functions, respectively. They are very clear and easy to use and combine with other packages like dplyr.
To show the basic usage of UCSCXenaTools, we will download clinical data of LUNG, LUAD, LUSC from TCGA (hg19 version) data hub. Users can learn more about UCSCXenaTools by running browseVignettes("UCSCXenaTools") to read vignette.
UCSCXenaTools uses a data.frame object (built in package) XenaData to generate an instance of XenaHub class, which records information of all datasets of UCSC Xena Data Hubs.
You can load XenaData after loading UCSCXenaTools into R.
-library(UCSCXenaTools)
-#> =========================================================================================
-#> UCSCXenaTools version 1.4.7
-#> Project URL: https://github.com/ropensci/UCSCXenaTools
-#> Usages: https://cran.r-project.org/web/packages/UCSCXenaTools/vignettes/USCSXenaTools.html
-#>
-#> If you use it in published research, please cite:
-#> Wang et al., (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data
-#> from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
-#> Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627
-#> =========================================================================================
-#> --Enjoy it--
-data(XenaData)
-
-head(XenaData)
-#> # A tibble: 6 × 17
-#> XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label
-#> <chr> <chr> <chr> <chr> <int> <chr> <chr>
-#> 1 https://… publicHub Breast Can… ucsfNeve_pu… 51 gene expre… Neve…
-#> 2 https://… publicHub Breast Can… ucsfNeve_pu… 57 phenotype Phen…
-#> 3 https://… publicHub Glioma (Ko… kotliarov20… 194 copy number Kotl…
-#> 4 https://… publicHub Glioma (Ko… kotliarov20… 194 phenotype Phen…
-#> 5 https://… publicHub Lung Cance… weir2007_pu… 383 copy number CGH
-#> 6 https://… publicHub Lung Cance… weir2007_pu… 383 phenotype Phen…
-#> # … with 10 more variables: Type <chr>, AnatomicalOrigin <chr>,
-#> # SampleType <chr>, Tags <chr>, ProbeMap <chr>, LongTitle <chr>,
-#> # Citation <chr>, Version <chr>, Unit <chr>, Platform <chr>Select datasets.
-
-# The options in XenaFilter function support Regular Expression
-XenaGenerate(subset = XenaHostNames=="tcgaHub") %>%
- XenaFilter(filterDatasets = "clinical") %>%
- XenaFilter(filterDatasets = "LUAD|LUSC|LUNG") -> df_todo
-
-df_todo
-#> class: XenaHub
-#> hosts():
-#> https://tcga.xenahubs.net
-#> cohorts() (3 total):
-#> TCGA Lung Cancer (LUNG)
-#> TCGA Lung Adenocarcinoma (LUAD)
-#> TCGA Lung Squamous Cell Carcinoma (LUSC)
-#> datasets() (3 total):
-#> TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
-#> TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
-#> TCGA.LUSC.sampleMap/LUSC_clinicalMatrixQuery and download.
-
-XenaQuery(df_todo) %>%
- XenaDownload() -> xe_downloadFor researchers in China, now Hiplot team has deployed several Xena mirror sites (https://xena.hiplot.com.cn/) at Shanghai. You can set an option options(use_hiplot = TRUE) before querying data step to speed up both data querying and downloading.
-options(use_hiplot = TRUE)
-
-XenaQuery(df_todo) %>%
- XenaDownload() -> xe_download
-#> The hiplot server may down, we will not use it for now.
-#> This will check url status, please be patient.
-#> All downloaded files will under directory C:\Users\ADMINI~1\AppData\Local\Temp\RtmpIfw2E2.
-#> The 'trans_slash' option is FALSE, keep same directory structure as Xena.
-#> Creating directories for datasets...
-#> Downloading TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
-#> Downloading TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
-#> Downloading TCGA.LUSC.sampleMap/LUSC_clinicalMatrixPrepare data into R for analysis.
-
-cli = XenaPrepare(xe_download)
-class(cli)
-#> [1] "list"
-names(cli)
-#> [1] "LUNG_clinicalMatrix" "LUAD_clinicalMatrix" "LUSC_clinicalMatrix"Cite me by the following paper.
-Wang et al., (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data
- from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
- Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627
-
-# For BibTex
-
-@article{Wang2019UCSCXenaTools,
- journal = {Journal of Open Source Software},
- doi = {10.21105/joss.01627},
- issn = {2475-9066},
- number = {40},
- publisher = {The Open Journal},
- title = {The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq},
- url = {https://dx.doi.org/10.21105/joss.01627},
- volume = {4},
- author = {Wang, Shixiang and Liu, Xuesong},
- pages = {1627},
- date = {2019-08-05},
- year = {2019},
- month = {8},
- day = {5},
-}Cite UCSC Xena by the following paper.
-Goldman, Mary, et al. "The UCSC Xena Platform for cancer genomics data
- visualization and interpretation." BioRxiv (2019): 326470.For anyone who wants to contribute, please follow the guideline:
-UCSCXenaTools.Rproj with RStudiodevtools::check(), and fix all errors, warnings and notes
NEWS.md
- XenaData.[1] "TCGA_survival_data_2.txt"
-[2] "clinical_CellLinePolyA_21.06_2021-06-15.tsv"
-[3] "CellLinePolyA_21.06_hugo_log2tpm_58581genes_2021-06-15.tsv"fetch().url_encode() is added internally to transform reserved characters (/ is kept).XenaQuery() and thus change the column number. This bug will not affect XenaTools itself.XenaQuery() and thus change the column order. This bug will not affect XenaTools itself.fetch() functions.https://xena.hiplot.com.cn/).fetch_sparse_values() function.R/XenaBrowse.R
- XenaBrowse.RdThis will open dataset/cohort link of UCSC Xena -in user's default browser.
-XenaBrowse(x, type = c("dataset", "cohort"), multiple = FALSE)a XenaHub object.
one of "dataset" and "cohort".
if TRUE, browse multiple links instead of throwing error.
# \donttest{
-XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
- XenaFilter(filterDatasets = "clinical") %>%
- XenaFilter(filterDatasets = "LUAD") -> to_browse
-# }
-This data.frame is very useful for selecting datasets fastly and
-independent on APIs of UCSC Xena Hubs.
A tibble.
Generated from UCSC Xena Data Hubs.
-R/XenaHub-class.R
- XenaDataUpdate.RdGet or Update Newest Data Information of UCSC Xena Data Hubs
-XenaDataUpdate(saveTolocal = TRUE)logical. Whether save to local R package data directory for permanent use -or Not.
a data.frame contains all datasets information of Xena.
if (FALSE) {
-XenaDataUpdate()
-XenaDataUpdate(saveTolocal = TRUE)
-}
-Avaliable datasets list: https://xenabrowser.net/datapages/
-XenaDownload(
- xquery,
- destdir = tempdir(),
- download_probeMap = FALSE,
- trans_slash = FALSE,
- force = FALSE,
- max_try = 3L,
- ...
-)a tibble object generated by XenaQuery function.
specify a location to store download data. Default is system temp directory.
if TRUE, also download ProbeMap data, which used for id mapping.
logical, default is FALSE. If TRUE, transform slash '/' in dataset id
-to '__'. This option is for backwards compatibility.
logical. if TRUE, force to download data no matter whether files exist.
-Default is FALSE.
time limit to try downloading the data.
other argument to download.file function
a tibble
if (FALSE) {
-xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
-hosts(xe)
-xe_query = XenaQuery(xe)
-xe_download = XenaDownload(xe_query)
-}
-One of main functions in UCSCXenatools. It is used to filter
-XenaHub object according to cohorts, datasets. All datasets can be found
-at https://xenabrowser.net/datapages/.
XenaFilter(
- x,
- filterCohorts = NULL,
- filterDatasets = NULL,
- ignore.case = TRUE,
- ...
-)a XenaHub object
default is NULL. A character used to filter cohorts,
-regular expression is supported.
default is NULL. A character used to filter datasets,
-regular expression is supported.
if FALSE, the pattern matching is case sensitive
-and if TRUE, case is ignored during matching.
other arguments except value passed to base::grep().
a XenaHub object
# operate TCGA datasets
-xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
-xe
-# get all names of clinical data
-xe2 = XenaFilter(xe, filterDatasets = "clinical")
-datasets(xe2)
-R/XenaGenerate.R
- XenaGenerate.RdGenerate and Subset a XenaHub Object from 'XenaData'
-XenaGenerate(XenaData = UCSCXenaTools::XenaData, subset = TRUE)a data.frame. Default is data(XenaData).
-The input of this option can only be data(XenaData) or its subset.
logical expression indicating elements or rows to keep.
a XenaHub object.
-# 1 get all datasets
-XenaGenerate()
-# 2 get TCGA BRCA
-XenaGenerate(subset = XenaCohorts == "TCGA Breast Cancer (BRCA)")
-# 3 get all datasets containing BRCA
-XenaGenerate(subset = grepl("BRCA", XenaCohorts))
-a S4 class to represent UCSC Xena Data Hubs
-hostshosts of data hubs
cohortscohorts of data hubs
datasetsdatasets of data hubs
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/.
XenaHub(
- hosts = xena_default_hosts(),
- cohorts = character(),
- datasets = character(),
- hostName = c("publicHub", "tcgaHub", "gdcHub", "icgcHub", "toilHub",
- "pancanAtlasHub", "treehouseHub", "pcawgHub", "atacseqHub", "singlecellHub",
- "kidsfirstHub")
-)a character vector specify UCSC Xena hosts, all available hosts can be
-found by xena_default_hosts() function. hostName is a more recommend option.
default is empty character vector, all cohorts will be returned.
default is empty character vector, all datasets will be returned.
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.
a XenaHub object
-Prepare (Load) Downloaded Datasets to R
-XenaPrepare(
- objects,
- objectsName = NULL,
- use_chunk = FALSE,
- chunk_size = 100,
- subset_rows = TRUE,
- select_cols = TRUE,
- callback = NULL,
- comment = "#",
- na = c("", "NA", "[Discrepancy]"),
- ...
-)a object of character vector or data.frame. If objects is data.frame,
-it should be returned object of XenaDownload function. More easier way is
-that objects can be character vector specify local files/directory and download urls.
specify names for elements of return object, i.e. names of list
default is FALSE. If you want to select subset of original data, please set it to
-TRUE and specify corresponding arguments: chunk_size, select_direction, select_names,
-callback.
the number of rows to include in each chunk
logical expression indicating elements or rows to keep:
-missing values are taken as false. x can be a representation of data frame
-you wanna do subset operation. Of note, the first colname of most of datasets
-in Xena will be set to "sample", you can use it to select rows.
expression, indicating columns to select from a data frame.
-'x' can be a representation of data frame you wanna do subset operation,
-e.g. select_cols = colnames(x)[1:3] will keep only first to third column.
a function to call on each chunk, default is NULL,
-this option will overvide operations of subset_rows and select_cols.
a character specify comment rows in files
a character vectory specify NA values in files
other arguments transfer to read_tsv function or
-read_tsv_chunked function (when use_chunk is TRUE) of readr package.
a list contains file data, which in way of tibbles
-if (FALSE) {
-xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
-hosts(xe)
-xe_query = XenaQuery(xe)
-
-xe_download = XenaDownload(xe_query)
-dat = XenaPrepare(xe_download)
-}
-Query URL of Datasets before Downloading
-XenaQuery(x)a XenaHub object
a data.frame contains hosts, datasets and url
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
-hosts(xe)
-if (FALSE) {
-xe_query = XenaQuery(xe)
-}
-If dataset has no ProbeMap, it will be ignored.
-XenaQueryProbeMap(x)a XenaHub object
a data.frame contains hosts, datasets and url
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
-hosts(xe)
-if (FALSE) {
-xe_query = XenaQueryProbeMap(xe)
-}
-R/XenaScan.R
- XenaScan.RdXenaScan() is a function can be used before XenaGenerate().
XenaScan(
- XenaData = UCSCXenaTools::XenaData,
- pattern = NULL,
- ignore.case = TRUE
-)a data.frame. Default is data(XenaData).
-The input of this option can only be data(XenaData) or its subset.
character string containing a regular expression
- (or character string for fixed = TRUE) to be matched
- in the given character vector. Coerced by
- as.character to a character string if possible. If a
- character vector of length 2 or more is supplied, the first element
- is used with a warning. Missing values are allowed except for
- regexpr, gregexpr and regexec.
if FALSE, the pattern matching is case
- sensitive and if TRUE, case is ignored during matching.
a data.frame
-x1 <- XenaScan(pattern = "Blood")
-x2 <- XenaScan(pattern = "LUNG", ignore.case = FALSE)
-
-x1 %>%
- XenaGenerate()
-x2 %>%
- XenaGenerate()
-Xena Shiny App
-XenaShiny()R/simplify.R
- availTCGA.RdGet or Check TCGA Available ProjectID, DataType and FileType
-availTCGA(which = c("all", "ProjectID", "DataType", "FileType"))a character of c("All", "ProjectID", "DataType", "FileType")
# \donttest{
-availTCGA("all")
-# }
-Get cohorts of XenaHub object
-cohorts(x)a XenaHub object
a character vector contains cohorts
-xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); cohorts(xe)
-Get datasets of XenaHub object
-datasets(x)a XenaHub object
a character vector contains datasets
-xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); datasets(xe)
-TCGA is a very useful database and here we provide this function to -download TCGA (include TCGA Pancan) datasets in human-friendly way. Users who are not -familiar with R operation will benefit from this.
-downloadTCGA(
- project = NULL,
- data_type = NULL,
- file_type = NULL,
- destdir = tempdir(),
- force = FALSE,
- ...
-)default is NULL. Should be one or more of TCGA project id (character vector) provided by Xena.
-See all available project id, please use availTCGA("ProjectID").
default is NULL. Should be a character vector specify data type.
-See all available data types by availTCGA("DataType").
default is NULL. Should be a character vector specify file type.
-See all available file types by availTCGA("FileType").
specify a location to store download data. Default is system temp directory.
logical. if TRUE, force to download data no matter whether files exist.
-Default is FALSE.
other argument to download.file function
same as XenaDownload() function result.
All availble information about datasets of TCGA can access vis availTCGA() and
-check with showTCGA().
if (FALSE) {
-# download RNASeq data (use UVM as example)
-downloadTCGA(project = "UVM",
- data_type = "Gene Expression RNASeq",
- file_type = "IlluminaHiSeq RNASeqV2")
-}
-When you want to query just data for several genes/samples from UCSC Xena datasets, a better way
-is to use these fetch_ functions instead of downloading a whole dataset. Details about functions
-please see the following sections.
fetch(host, dataset)
-
-fetch_dense_values(
- host,
- dataset,
- identifiers = NULL,
- samples = NULL,
- check = TRUE,
- use_probeMap = FALSE,
- time_limit = 30
-)
-
-fetch_sparse_values(host, dataset, genes, samples = NULL, time_limit = 30)
-
-fetch_dataset_samples(host, dataset, limit = NULL)
-
-fetch_dataset_identifiers(host, dataset)
-
-has_probeMap(host, dataset, return_url = FALSE)a UCSC Xena host, like "https://toil.xenahubs.net".
-All available hosts can be printed by xena_default_hosts().
a UCSC Xena dataset, like "tcga_RSEM_gene_tpm".
-All available datasets can be printed by running XenaData$XenaDatasets or
-obtained from UCSC Xena datapages.
Identifiers could be probe (like "ENSG00000000419.12"),
-gene (like "TP53") etc.. If it is NULL, all identifiers in the dataset will be used.
ID of samples, like "TCGA-02-0047-01".
-If it is NULL, all samples in the dataset will be used. However, it is better to download
-the whole datasets if you query many samples and genes.
if TRUE, check whether specified identifiers and samples exist the dataset
-(all failed items will be filtered out). However, if FALSE, the code is much faster.
if TRUE, will check if the dataset has ProbeMap firstly.
-When the dataset you want to query has a identifier-to-gene mapping, identifiers can be
-gene symbols even the identifiers of dataset are probes or others.
time limit for getting response in seconds.
gene names.
number of samples, if NULL, return all samples.
if TRUE, returns the info of probeMap
-instead of a logical value when the result exists.
a matirx or character vector or a list.
There are three primary data types: dense matrix (samples by probes (or say identifiers)), -sparse (sample, position, variant), and segmented (sample, position, value).
-Dense matrices can be genotypic or phenotypic, it is a sample-by-identifiers matrix. -Phenotypic matrices have associated field metadata (descriptive names, codes, etc.). -Genotypic matricies may have an associated probeMap, which maps probes to genomic locations. -If a matrix has hugo probeMap, the probes themselves are gene names. Otherwise, a probeMap is -used to map a gene location to a set of probes.
-fetch_dense_values: fetches values from a dense matrix.
fetch_sparse_values: fetches values from a sparse data.frame.
fetch_dataset_samples: fetches samples from a dataset
fetch_dataset_identifiers: fetches identifies from a dataset.
has_probeMap: checks if a dataset has ProbeMap.
library(UCSCXenaTools)
-
-host <- "https://toil.xenahubs.net"
-dataset <- "tcga_RSEM_gene_tpm"
-samples <- c("TCGA-02-0047-01", "TCGA-02-0055-01", "TCGA-02-2483-01", "TCGA-02-2485-01")
-probes <- c("ENSG00000282740.1", "ENSG00000000005.5", "ENSG00000000419.12")
-genes <- c("TP53", "RB1", "PIK3CA")
-
-# \donttest{
-# Fetch samples
-fetch_dataset_samples(host, dataset, 2)
-# Fetch identifiers
-fetch_dataset_identifiers(host, dataset)
-# Fetch expression value by probes
-fetch_dense_values(host, dataset, probes, samples, check = FALSE)
-# Fetch expression value by gene symbol (if the dataset has probeMap)
-has_probeMap(host, dataset)
-fetch_dense_values(host, dataset, genes, samples, check = FALSE, use_probeMap = TRUE)
-# }
-This is the most useful function for user to download common
-TCGA datasets, it is similar to getFirehoseData function in RTCGAToolbox
-package.
getTCGAdata(
- project = NULL,
- clinical = TRUE,
- download = FALSE,
- forceDownload = FALSE,
- destdir = tempdir(),
- mRNASeq = FALSE,
- mRNAArray = FALSE,
- mRNASeqType = "normalized",
- miRNASeq = FALSE,
- exonRNASeq = FALSE,
- RPPAArray = FALSE,
- ReplicateBaseNormalization = FALSE,
- Methylation = FALSE,
- MethylationType = c("27K", "450K"),
- GeneMutation = FALSE,
- SomaticMutation = FALSE,
- GisticCopyNumber = FALSE,
- Gistic2Threshold = TRUE,
- CopyNumberSegment = FALSE,
- RemoveGermlineCNV = TRUE,
- ...
-)default is NULL. Should be one or more of TCGA project id (character vector) provided by Xena.
-See all available project id, please use availTCGA("ProjectID").
logical. if TRUE, download clinical information. Default is TRUE.
logical. if TRUE, download data, otherwise return a result list include data
-information. Default is FALSE. You can set this to FALSE if you want to check what you will download or
-use other function provided by UCSCXenaTools to filter result datasets you want to download.
logical. if TRUE, force to download files no matter if exist. Default is FALSE.
specify a location to store download data. Default is system temp directory.
logical. if TRUE, download mRNASeq data. Default is FALSE.
logical. if TRUE, download mRNA microarray data. Default is FALSE.
character vector. Can be one, two or three
-in c("normalized", "pancan normalized", "percentile").
logical. if TRUE, download miRNASeq data. Default is FALSE.
logical. if TRUE, download exon RNASeq data. Default is FALSE.
logical. if TRUE, download RPPA data. Default is FALSE.
logical. if TRUE, download RPPA data by Replicate Base
-Normalization (RBN). Default is FALSE.
logical. if TRUE, download DNA Methylation data. Default is FALSE.
character vector. Can be one or two in c("27K", "450K").
logical. if TRUE, download gene mutation data. Default is FALSE.
logical. if TRUE, download somatic mutation data. Default is FALSE.
logical. if TRUE, download Gistic2 Copy Number data. Default is FALSE.
logical. if TRUE, download Threshold Gistic2 data. Default is TRUE.
logical. if TRUE, download Copy Number Segment data. Default is FALSE.
logical. if TRUE, download Copy Number Segment data which has removed
-germline copy number variation. Default is TRUE.
other argument to download.file function
if download=TRUE, return data.frame from XenaDownload,
-otherwise return a list including XenaHub object and datasets information
TCGA Common Data Sets are frequently used for biological analysis.
-To make easier to achieve these data, this function provide really easy
-options to choose datasets and behavior. All availble information about
-datasets of TCGA can access vis availTCGA() and check with showTCGA().
###### get data, but not download
-
-# 1 choose project and data types you wanna download
-getTCGAdata(project = "LUAD", mRNASeq = TRUE, mRNAArray = TRUE,
-mRNASeqType = "normalized", miRNASeq = TRUE, exonRNASeq = TRUE,
-RPPAArray = TRUE, Methylation = TRUE, MethylationType = "450K",
-GeneMutation = TRUE, SomaticMutation = TRUE)
-
-# 2 only choose 'LUAD' and its clinical data
-getTCGAdata(project = "LUAD")
-if (FALSE) {
-###### download datasets
-
-# 3 download clinical datasets of LUAD and LUSC
-getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, download = TRUE)
-
-# 4 download clinical, RPPA and gene mutation datasets of LUAD and LUSC
-# getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, RPPAArray = TRUE, GeneMutation = TRUE)
-}
-Get hosts of XenaHub object
-hosts(x)a XenaHub object
a character vector contains hosts
-xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); hosts(xe)
-
- Standard dataset query and download pipeline-Select, query, download and load datasets. - |
- |
|---|---|
| - - | -Xena Hub Information |
-
| - - | -Scan all rows according to user input by a regular expression |
-
| - - | -Generate and Subset a XenaHub Object from 'XenaData' |
-
| - - | -Filter a XenaHub Object |
-
| - - | -View Info of Dataset or Cohort at UCSC Xena Website Using Web browser |
-
| - - | -Query URL of Datasets before Downloading |
-
| - - | -Download Datasets from UCSC Xena Hubs |
-
| - - | -Prepare (Load) Downloaded Datasets to R |
-
- Download a subset of dataset-Download a subset of dataset for target analysis. - |
- |
|
-
|
- Fetch Data from UCSC Xena Hosts |
-
- One-click download function-Download datasets by setting options in one function. - |
- |
| - - | -Easily Download TCGA Data by Several Options |
-
| - - | -Get TCGA Common Data Sets by Project ID and Property |
-
| - - | -Get or Check TCGA Available ProjectID, DataType and FileType |
-
| - - | -Show TCGA data structure by Project ID or ALL |
-
- Utility-Useful functions. - |
- |
| - - | -Get or Update Newest Data Information of UCSC Xena Data Hubs |
-
| - - | -Xena Shiny App |
-
| - - | -Get hosts of XenaHub object |
-
| - - | -Get cohorts of XenaHub object |
-
| - - | -Get datasets of XenaHub object |
-
| - - | -Get Samples of a XenaHub object according to 'by' and 'how' action arguments |
-
|
-
|
- Fetch Data from UCSC Xena Hosts |
-
| - - | -Query ProbeMap URL of Datasets |
-
- Helpers-Helper functions. - |
- |
| - - | -UCSC Xena Default Hosts |
-
| - - | -Convert camel case to snake case |
-
- Class-Class and related function. - |
- |
| - - | -Class XenaHub |
-
| - - | -Generate a XenaHub Object |
-
See magrittr::%>% for details.
lhs %>% rhsR/api_higher.R
- samples.RdOne is often interested in identifying samples or features present in each data set, -or shared by all data sets, or present in any of several data sets. -Identifying these samples, including samples in arbitrarily chosen data sets.
-a XenaHub object
default is a empty character, it is used to specify
-the host, cohort or dataset by by option otherwise
-info will be automatically extracted by code
a character specify by action
a character specify how action
a list include samples
-This can used to check if data type or file type exist in one or more projects by hand.
-showTCGA(project = "all")a character vector. Can be "all" or one or more of TCGA Project IDs.
a data.frame including project data structure information.
# \donttest{
-showTCGA("all")
-# }
-Convert camel case to snake case
-to_snake(name)a character vector
same length as name but with snake case
to_snake("sparseDataRange")
-Return Xena default hosts
-xena_default_hosts()A character vector include current defalut hosts
-