clinicalomicsdbR

R package for interfacing with ClinicalOmicsDB

https://github.com/bzhanglab/clinicalomicsdbr

Repository

R package for interfacing with ClinicalOmicsDB

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# clinicalomicsdbR


[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.8239443.svg)](https://doi.org/10.5281/zenodo.8239443)


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

``` r
install.packages("clinicalomicsdbR")
```

You can install the development version of clinicalomicsdbR from [GitHub](https://github.com/) with:

``` r
# 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 the `filter()` function.

## Functions

- `new()` - Create new clinicalomicsdbR object. Needed before any other
  function
- `filter(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 from `filter()` into
  `output_dir`.
- `dataframe()` - loads all the studies from `filter()` into a
  list, with column `study_list` that contains the names of the
  studies and `df` that contains a list of the study data information.
- `dataframe_from_id(study_id)` - loads a study with id from `study_id` into a dataframe
- `download_from_id(study_id, output_dir)` - downsloads a study with id from `study_id` into a folder `output_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.

```{r example}
library(clinicalomicsdbR)

clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$download(output_dir = tempdir()) # downloads all files
```

### 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`.

``` {r}
library(clinicalomicsdbR)

res <- clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$dataframe(); # downloads all files

for (study in res[["study_list"]]) {
  print(ncol(res[["df"]][[study]]))
}
```

Owner

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: clinicalomicsdbR
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: John Michael
    family-names: Elizarraras
    affiliation: Baylor College of Medicine
identifiers:
  - type: doi
    value: 10.5281/zenodo.8239443
    description: Zenodo DOI
repository-code: 'https://github.com/bzhanglab/clinicalomicsdbR'
url: 'http://trials.linkedomics.org/'
repository: 'https://zenodo.org/records/8252813'
abstract: >-
  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>.
keywords:
  - bioinformatics
  - omics
  - biology
license: MIT
preferred-citation:
  type: article
  authors:
  - given-names: Chang In
    family-names: Moon
    affiliation: Baylor College of Medicine
  - given-names: John Michael
    family-names: Elizarraras
    affiliation: Baylor College of Medicine
  - given-names: Jonathan Thomas
    family-names: Lei
    affiliation: Baylor College of Medicine
  - given-names: Byron
    family-names: Jia
    affiliation: Carleton College
  - given-names: Bing
    family-names: Zhang
    affiliation: Baylor College of Medicine
  doi: 10.1093/nar/gkad871
  journal: "Nucleic Acids Research"
  month: 1
  title: "ClinicalOmicsDB: exploring molecular associations of oncology drug responses in clinical trials"
  issue: D1
  volume: 52
  year: 2024

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