Description
Interface with the 'ClinicalOmicsDB' API, Allowing for Easy Data Downloading and Importing.
Description
Provides an interface to the 'ClinicalOmicsDB' API, allowing for easy data downloading and importing. 'ClinicalOmicsDB' is a database of clinical and 'omics' data from cancer patients. The database is accessible at <http://trials.linkedomics.org>.
README.md
clinicalomicsdbR
R package to interface with the ClinicalOmicsDB API. Can be used to download data for your own analysis, or directly load study information into a dataframe for exploration.
Designed with the structure from https://r-pkgs.org/.
Installation
To install the latest stable release, run
install.packages("clinicalomicsdbR")
You can install the development version of clinicalomicsdbR from GitHub with:
# install.packages("devtools")
devtools::install_github("bzhanglab/clinicalomicsdbR")
See Examples below to see how to use.
Parameters
hostname
- base URL of the website containing the ClinicalOmicsDB API. Only change if you are running a custom service.study_list
- list containing all the studies that were filtered by thefilter()
function.
Functions
new()
- Create new clinicalomicsdbR object. Needed before any other functionfilter(drugs, cancers)
- filters studies matching provided arguments.drugs
is a list and can be individual drugs or combinations. See the ClinicalOmicsDB website for all options.cancers
can contain multiple cancers.download(output_dir)
- downloads all studies fromfilter()
intooutput_dir
.dataframe()
- loads all the studies fromfilter()
into a list, with columnstudy_list
that contains the names of the studies anddf
that contains a list of the study data information.dataframe_from_id(study_id)
- loads a study with id fromstudy_id
into a dataframedownload_from_id(study_id, output_dir)
- downsloads a study with id fromstudy_id
into a folderoutput_dir
. See the examples below for more information on how to use.
Examples
Filter and Download
Filters studies for those which used rituximab or ipilimumab then downloads them to the studies
folder.
library(clinicalomicsdbR)
clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$download(output_dir = tempdir()) # downloads all files
#> Filtered to 4 studies.
#> Downloading study Gide_Cell_2019_pembro_ipi.csv from https://bcm.box.com/shared/static/swf5fywqcqmf75600g7v8irt2a9agnqo.csv
#> Downloading study VanAllen_antiCTLA4_2015.csv from https://bcm.box.com/shared/static/v0sphd7ht487qk96xbwjokgkbkjpexom.csv
#> Downloading study Gide_Cell_2019_nivo_ipi.csv from https://bcm.box.com/shared/static/jwv108f6cy4kvyeqer95jdugla53m1zt.csv
#> Downloading study GSE35935.csv from https://bcm.box.com/shared/static/8icr4i6gbbp6lgd01iscbss4v7lnj6c5.csv
#> Downloaded 4 studies.
Filter and Get Data Frame
Filters studies for those which used rituximab or ipilimumab then gets data frame.
Notes: output_dir
is optional. Defaults to clindb
.
library(clinicalomicsdbR)
res <- clinicalomicsdbR$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