Package 'clinicalomicsdbR'

Title: 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>.
Authors: John Elizarraras [aut, cre, ctb]
Maintainer: John Elizarraras <[email protected]>
License: MIT + file LICENSE
Version: 1.0.5.9000
Built: 2025-02-22 04:09:54 UTC
Source: https://github.com/bzhanglab/clinicalomicsdbr

Help Index

clinicalomicsdbR object

Description

clinicalomicsdbR object

clinicalomicsdbR object

Value

Returns a new clinicalomicsdbR object

Public fields

hostname

The url of the API to connect to. Only change if you are using a custom service.

study_list

The list of all the studies that are a result of filtering.

verbosity

The level of messages wanted for downloads (defaults to 0: No Output). Follows httr2 documentatation for req_perform

Methods

Public methods

Method filter()

filter objects according to the specified drugs and cancers

Usage
clinicalomicsdbR$filter(drugs = c(), cancers = c())
Arguments
drugs

list or vector containing drugs that studies need to contain at least one of

cancers

list of vector of cancer types to consider. Leave empty to consider all cancer types

Returns

new clinicalomicsdbR object with the filtered results in ⁠$study_list⁠

Method get_download_url()

Get download url for a study at specified study_id

Usage
clinicalomicsdbR$get_download_url(study_id)
Arguments
study_id

String of the ID of the study to get the download url of

Returns

String of the download url

Method download()

Download all files of the studies in self$study_list. Use filter function first

Usage
clinicalomicsdbR$download(output_dir)
Arguments
output_dir

Directory to download files to.

Returns

unmodifed clinicalomicsdbR object

Method download_from_id()

Download all file from study_id into output_dir directory

Usage
clinicalomicsdbR$download_from_id(study_id)
Arguments
study_id

String containing the ID of the study to download

output_dir

Directory to download files to.

Returns

unmodifed clinicalomicsdbR object

Method dataframe()

Get all files of the studies in self$study_list and load into data frame. Use filter function first.

Usage
clinicalomicsdbR$dataframe()
Returns

list with study_list element to display all studies and list df with each dataframe in the list

Method dataframe_from_id()

Get file from study_id and convert into dataframe.

Usage
clinicalomicsdbR$dataframe_from_id(study_id)
Arguments
study_id

String containing the ID of the study to get dataframe of

Returns

data frame containing data of study

Method clone()

The objects of this class are cloneable with this method.

Usage
clinicalomicsdbR$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$study_list # downloads all files