From e443773f66e923b8feed51c4c7d51df911157aed Mon Sep 17 00:00:00 2001
From: iblacksand <iblacksand@users.noreply.github.com>
Date: Wed, 26 Jun 2024 14:53:09 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bzhangla?=
 =?UTF-8?q?b/clinicalomicsdbR@61ecfeab99d752fc032abaec3d317f8dd8cd5f6d=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
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Content-Transfer-Encoding: 8bit

---
 index.html      | 1 +
 news/index.html | 2 +-
 pkgdown.yml     | 2 +-
 search.json     | 2 +-
 4 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/index.html b/index.html
index 029da40..8db7fab 100644
--- a/index.html
+++ b/index.html
@@ -154,6 +154,7 @@ <h3 id="filter-and-get-data-frame">Filter and Get Data Frame<a class="anchor" ar
   </main><aside class="col-md-3"><div class="links">
 <h2 data-toc-skip>Links</h2>
 <ul class="list-unstyled">
+<li><a href="https://cloud.r-project.org/package=clinicalomicsdbR" class="external-link">View on CRAN</a></li>
 <li><a href="https://github.com/bzhanglab/clinicalomicsdbR/" class="external-link">Browse source code</a></li>
 <li><a href="https://github.com/bzhanglab/clinicalomicsdbR/issues" class="external-link">Report a bug</a></li>
 </ul>
diff --git a/news/index.html b/news/index.html
index 502f451..5dfd8b8 100644
--- a/news/index.html
+++ b/news/index.html
@@ -45,7 +45,7 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="1.0.5" id="clinicalomicsdbr-105">clinicalomicsdbR 1.0.5<a class="anchor" aria-label="anchor" href="#clinicalomicsdbr-105"></a></h2>
+<h2 class="pkg-version" data-toc-text="1.0.5" id="clinicalomicsdbr-105">clinicalomicsdbR 1.0.5<a class="anchor" aria-label="anchor" href="#clinicalomicsdbr-105"></a></h2><p class="text-muted">CRAN release: 2024-06-26</p>
 </div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.0.4" id="clinicalomicsdbr-104">clinicalomicsdbR 1.0.4<a class="anchor" aria-label="anchor" href="#clinicalomicsdbr-104"></a></h2>
diff --git a/pkgdown.yml b/pkgdown.yml
index 718fa20..503e9b5 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-06-25T14:58Z
+last_built: 2024-06-26T14:53Z
 urls:
   reference: https://bzhanglab.github.io/clinicalomicsdbR/reference
   article: https://bzhanglab.github.io/clinicalomicsdbR/articles
diff --git a/search.json b/search.json
index 61ce423..f186ff4 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://bzhanglab.github.io/clinicalomicsdbR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 clinicalomicsdbR authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Elizarraras. Author, maintainer, contributor.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Elizarraras J (2024). clinicalomicsdbR: Interface 'ClinicalOmicsDB' API, Allowing Easy Data Downloading Importing. R package version 1.0.5, https://github.com/bzhanglab/clinicalomicsdbR.","code":"@Manual{,   title = {clinicalomicsdbR: Interface with the 'ClinicalOmicsDB' API, Allowing for Easy Data Downloading and Importing},   author = {John Elizarraras},   year = {2024},   note = {R package version 1.0.5},   url = {https://github.com/bzhanglab/clinicalomicsdbR}, }"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"clinicalomicsdbr","dir":"","previous_headings":"","what":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"R package interface ClinicalOmicsDB API. Can used download data analysis, directly load study information dataframe exploration. Designed structure https://r-pkgs.org/.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"install latest stable release, run can install development version clinicalomicsdbR GitHub : See Examples see use.","code":"install.packages(\"clinicalomicsdbR\") # install.packages(\"devtools\") devtools::install_github(\"bzhanglab/clinicalomicsdbR\")"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"parameters","dir":"","previous_headings":"","what":"Parameters","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"hostname - base URL website containing ClinicalOmicsDB API. change running custom service. study_list - list containing studies filtered filter() function.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"functions","dir":"","previous_headings":"","what":"Functions","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"new() - Create new clinicalomicsdbR object. Needed function filter(drugs, cancers) - filters studies matching provided arguments. drugs list can individual drugs combinations. See ClinicalOmicsDB website options. cancers can contain multiple cancers. download(output_dir) - downloads studies filter() output_dir. dataframe() - loads studies filter() list, column study_list contains names studies df contains list study data information. dataframe_from_id(study_id) - loads study id study_id dataframe download_from_id(study_id, output_dir) - downsloads study id study_id folder output_dir. See examples information use.","code":""},{"path":[]},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"filter-and-download","dir":"","previous_headings":"Examples","what":"Filter and Download","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"Filters studies used rituximab ipilimumab downloads studies folder.","code":"library(clinicalomicsdbR)  clinicalomicsdbR$new()$filter(drugs = c(\"ipilimumab\", \"rituximab\"))$download(output_dir = tempdir()) # downloads all files #> Filtered to 4 studies. #> Downloading study Gide_Cell_2019_pembro_ipi.csv from https://bcm.box.com/shared/static/swf5fywqcqmf75600g7v8irt2a9agnqo.csv #> Downloading study VanAllen_antiCTLA4_2015.csv from https://bcm.box.com/shared/static/v0sphd7ht487qk96xbwjokgkbkjpexom.csv #> Downloading study Gide_Cell_2019_nivo_ipi.csv from https://bcm.box.com/shared/static/jwv108f6cy4kvyeqer95jdugla53m1zt.csv #> Downloading study GSE35935.csv from https://bcm.box.com/shared/static/8icr4i6gbbp6lgd01iscbss4v7lnj6c5.csv #> Downloaded 4 studies."},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"filter-and-get-data-frame","dir":"","previous_headings":"Examples","what":"Filter and Get Data Frame","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"Filters studies used rituximab ipilimumab gets data frame. Notes: output_dir optional. Defaults clindb.","code":"library(clinicalomicsdbR)  res <- clinicalomicsdbR$new()$filter(drugs = c(\"ipilimumab\", \"rituximab\"))$dataframe(); # downloads all files #> Filtered to 4 studies. #> Getting dataframe of study Gide_Cell_2019_pembro_ipi.csv from https://bcm.box.com/shared/static/swf5fywqcqmf75600g7v8irt2a9agnqo.csv #> Getting dataframe of study VanAllen_antiCTLA4_2015.csv from https://bcm.box.com/shared/static/v0sphd7ht487qk96xbwjokgkbkjpexom.csv #> Getting dataframe of study Gide_Cell_2019_nivo_ipi.csv from https://bcm.box.com/shared/static/jwv108f6cy4kvyeqer95jdugla53m1zt.csv #> Getting dataframe of study GSE35935.csv from https://bcm.box.com/shared/static/8icr4i6gbbp6lgd01iscbss4v7lnj6c5.csv for (study in res[[\"study_list\"]]) {   print(ncol(res[[\"df\"]][[study]])) } #> [1] 15194 #> [1] 15059 #> [1] 17145 #> [1] 20321"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":null,"dir":"Reference","previous_headings":"","what":"clinicalomicsdbR object — clinicalomicsdbR","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"clinicalomicsdbR object clinicalomicsdbR object","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Returns new clinicalomicsdbR object","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"hostname url API connect . change using custom service. study_list list studies result filtering. verbosity level messages wanted downloads (defaults 0: Output). Follows httr2 documentatation req_perform","code":""},{"path":[]},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"clinicalomicsdbR$filter() clinicalomicsdbR$get_download_url() clinicalomicsdbR$download() clinicalomicsdbR$download_from_id() clinicalomicsdbR$dataframe() clinicalomicsdbR$dataframe_from_id() clinicalomicsdbR$clone()","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-filter-","dir":"Reference","previous_headings":"","what":"Method filter()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"filter objects according specified drugs cancers","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$filter(drugs = c(), cancers = c())"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"drugs list vector containing drugs studies need contain least one cancers list vector cancer types consider. Leave empty consider cancer types","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"new clinicalomicsdbR object filtered results $study_list","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-get-download-url-","dir":"Reference","previous_headings":"","what":"Method get_download_url()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Get download url study specified study_id","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$get_download_url(study_id)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"study_id String ID study get download url ","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"String download url","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-download-","dir":"Reference","previous_headings":"","what":"Method download()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Download files studies self$study_list. Use filter function first","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$download(output_dir)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"output_dir Directory download files .","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"unmodifed clinicalomicsdbR object","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-download-from-id-","dir":"Reference","previous_headings":"","what":"Method download_from_id()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Download file study_id output_dir directory","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$download_from_id(study_id)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"study_id String containing ID study download output_dir Directory download files .","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"unmodifed clinicalomicsdbR object","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-dataframe-","dir":"Reference","previous_headings":"","what":"Method dataframe()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Get files studies self$study_list load data frame. Use filter function first.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$dataframe()"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"list study_list element display studies list df dataframe list","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-dataframe-from-id-","dir":"Reference","previous_headings":"","what":"Method dataframe_from_id()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Get file study_id convert dataframe.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$dataframe_from_id(study_id)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"study_id String containing ID study get dataframe ","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"data frame containing data study","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"objects class cloneable method.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$clone(deep = FALSE)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"deep Whether make deep clone.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$new()$filter(drugs = c(\"ipilimumab\", \"rituximab\"))$study_list # downloads all files #> Filtered to 4 studies. #> [1] \"Gide_Cell_2019_pembro_ipi.csv\" \"VanAllen_antiCTLA4_2015.csv\"   #> [3] \"Gide_Cell_2019_nivo_ipi.csv\"   \"GSE35935.csv\""},{"path":[]},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/news/index.html","id":"clinicalomicsdbr-104","dir":"Changelog","previous_headings":"","what":"clinicalomicsdbR 1.0.4","title":"clinicalomicsdbR 1.0.4","text":"Added NEWS.md file track changes package.","code":""}]
+[{"path":"https://bzhanglab.github.io/clinicalomicsdbR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 clinicalomicsdbR authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Elizarraras. Author, maintainer, contributor.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Elizarraras J (2024). clinicalomicsdbR: Interface 'ClinicalOmicsDB' API, Allowing Easy Data Downloading Importing. R package version 1.0.5, https://github.com/bzhanglab/clinicalomicsdbR.","code":"@Manual{,   title = {clinicalomicsdbR: Interface with the 'ClinicalOmicsDB' API, Allowing for Easy Data Downloading and Importing},   author = {John Elizarraras},   year = {2024},   note = {R package version 1.0.5},   url = {https://github.com/bzhanglab/clinicalomicsdbR}, }"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"clinicalomicsdbr","dir":"","previous_headings":"","what":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"R package interface ClinicalOmicsDB API. Can used download data analysis, directly load study information dataframe exploration. Designed structure https://r-pkgs.org/.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"install latest stable release, run can install development version clinicalomicsdbR GitHub : See Examples see use.","code":"install.packages(\"clinicalomicsdbR\") # install.packages(\"devtools\") devtools::install_github(\"bzhanglab/clinicalomicsdbR\")"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"parameters","dir":"","previous_headings":"","what":"Parameters","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"hostname - base URL website containing ClinicalOmicsDB API. change running custom service. study_list - list containing studies filtered filter() function.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"functions","dir":"","previous_headings":"","what":"Functions","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"new() - Create new clinicalomicsdbR object. Needed function filter(drugs, cancers) - filters studies matching provided arguments. drugs list can individual drugs combinations. See ClinicalOmicsDB website options. cancers can contain multiple cancers. download(output_dir) - downloads studies filter() output_dir. dataframe() - loads studies filter() list, column study_list contains names studies df contains list study data information. dataframe_from_id(study_id) - loads study id study_id dataframe download_from_id(study_id, output_dir) - downsloads study id study_id folder output_dir. See examples information use.","code":""},{"path":[]},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"filter-and-download","dir":"","previous_headings":"Examples","what":"Filter and Download","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"Filters studies used rituximab ipilimumab downloads studies folder.","code":"library(clinicalomicsdbR)  clinicalomicsdbR$new()$filter(drugs = c(\"ipilimumab\", \"rituximab\"))$download(output_dir = tempdir()) # downloads all files #> Filtered to 4 studies. #> Downloading study Gide_Cell_2019_pembro_ipi.csv from https://bcm.box.com/shared/static/swf5fywqcqmf75600g7v8irt2a9agnqo.csv #> Downloading study VanAllen_antiCTLA4_2015.csv from https://bcm.box.com/shared/static/v0sphd7ht487qk96xbwjokgkbkjpexom.csv #> Downloading study Gide_Cell_2019_nivo_ipi.csv from https://bcm.box.com/shared/static/jwv108f6cy4kvyeqer95jdugla53m1zt.csv #> Downloading study GSE35935.csv from https://bcm.box.com/shared/static/8icr4i6gbbp6lgd01iscbss4v7lnj6c5.csv #> Downloaded 4 studies."},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/index.html","id":"filter-and-get-data-frame","dir":"","previous_headings":"Examples","what":"Filter and Get Data Frame","title":"Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing","text":"Filters studies used rituximab ipilimumab gets data frame. Notes: output_dir optional. Defaults clindb.","code":"library(clinicalomicsdbR)  res <- clinicalomicsdbR$new()$filter(drugs = c(\"ipilimumab\", \"rituximab\"))$dataframe(); # downloads all files #> Filtered to 4 studies. #> Getting dataframe of study Gide_Cell_2019_pembro_ipi.csv from https://bcm.box.com/shared/static/swf5fywqcqmf75600g7v8irt2a9agnqo.csv #> Getting dataframe of study VanAllen_antiCTLA4_2015.csv from https://bcm.box.com/shared/static/v0sphd7ht487qk96xbwjokgkbkjpexom.csv #> Getting dataframe of study Gide_Cell_2019_nivo_ipi.csv from https://bcm.box.com/shared/static/jwv108f6cy4kvyeqer95jdugla53m1zt.csv #> Getting dataframe of study GSE35935.csv from https://bcm.box.com/shared/static/8icr4i6gbbp6lgd01iscbss4v7lnj6c5.csv for (study in res[[\"study_list\"]]) {   print(ncol(res[[\"df\"]][[study]])) } #> [1] 15194 #> [1] 15059 #> [1] 17145 #> [1] 20321"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":null,"dir":"Reference","previous_headings":"","what":"clinicalomicsdbR object — clinicalomicsdbR","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"clinicalomicsdbR object clinicalomicsdbR object","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Returns new clinicalomicsdbR object","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"hostname url API connect . change using custom service. study_list list studies result filtering. verbosity level messages wanted downloads (defaults 0: Output). Follows httr2 documentatation req_perform","code":""},{"path":[]},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"clinicalomicsdbR$filter() clinicalomicsdbR$get_download_url() clinicalomicsdbR$download() clinicalomicsdbR$download_from_id() clinicalomicsdbR$dataframe() clinicalomicsdbR$dataframe_from_id() clinicalomicsdbR$clone()","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-filter-","dir":"Reference","previous_headings":"","what":"Method filter()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"filter objects according specified drugs cancers","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$filter(drugs = c(), cancers = c())"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"drugs list vector containing drugs studies need contain least one cancers list vector cancer types consider. Leave empty consider cancer types","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"new clinicalomicsdbR object filtered results $study_list","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-get-download-url-","dir":"Reference","previous_headings":"","what":"Method get_download_url()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Get download url study specified study_id","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$get_download_url(study_id)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"study_id String ID study get download url ","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"String download url","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-download-","dir":"Reference","previous_headings":"","what":"Method download()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Download files studies self$study_list. Use filter function first","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$download(output_dir)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"output_dir Directory download files .","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"unmodifed clinicalomicsdbR object","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-download-from-id-","dir":"Reference","previous_headings":"","what":"Method download_from_id()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Download file study_id output_dir directory","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$download_from_id(study_id)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"study_id String containing ID study download output_dir Directory download files .","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"unmodifed clinicalomicsdbR object","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-dataframe-","dir":"Reference","previous_headings":"","what":"Method dataframe()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Get files studies self$study_list load data frame. Use filter function first.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$dataframe()"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"list study_list element display studies list df dataframe list","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-dataframe-from-id-","dir":"Reference","previous_headings":"","what":"Method dataframe_from_id()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"Get file study_id convert dataframe.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$dataframe_from_id(study_id)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"study_id String containing ID study get dataframe ","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"data frame containing data study","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"objects class cloneable method.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$clone(deep = FALSE)"},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"deep Whether make deep clone.","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/reference/clinicalomicsdbR.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"clinicalomicsdbR object — clinicalomicsdbR","text":"","code":"clinicalomicsdbR$new()$filter(drugs = c(\"ipilimumab\", \"rituximab\"))$study_list # downloads all files #> Filtered to 4 studies. #> [1] \"Gide_Cell_2019_pembro_ipi.csv\" \"VanAllen_antiCTLA4_2015.csv\"   #> [3] \"Gide_Cell_2019_nivo_ipi.csv\"   \"GSE35935.csv\""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/news/index.html","id":"clinicalomicsdbr-105","dir":"Changelog","previous_headings":"","what":"clinicalomicsdbR 1.0.5","title":"clinicalomicsdbR 1.0.5","text":"CRAN release: 2024-06-26","code":""},{"path":"https://bzhanglab.github.io/clinicalomicsdbR/news/index.html","id":"clinicalomicsdbr-104","dir":"Changelog","previous_headings":"","what":"clinicalomicsdbR 1.0.4","title":"clinicalomicsdbR 1.0.4","text":"Added NEWS.md file track changes package.","code":""}]