In mrblasco/CTE: Cancer Trial Explorer (CTE)

title: "Cancer Trials Explorer (CTE) -- examples" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{explorer} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(dplyr, warn = FALSE) # for data wrangling 
library(DT) # use datatables to format outcomes

The CTE library pulls data from several sources:

Filtering clinical trials

ClinicalTrials.gov hosts data for hundreds of thousand clinical trials (CTs) targeting a wide variety of conditions.

The goal of this library is to focus on CTs interventional (as opposed to observational) treating a cancer-related condition.

Accordingly, I included only CTs with terms related to cancer (e.g., cancer, tumor, leukemia, melanoma, glaucoma) in the conditions targeted by their intervention.

Data access

To access the data you first need to load the library.

library(CTE)

Then, the dataset is stored in separate files available in lazy mode (i.e., loaded when needed).

For example, to query the list of cancer-related clinical trials in the data you can type the following:

Clinical trial basic information

data(ct_info)
ct_info

Clinical trial list of associated interventions (e.g., drug treatments)

data(ct_interv)
ct_interv

Clinical trial list of associated targeted conditions

data(ct_cond)
ct_cond

Drug bank list of drugs

data(drugbank)
drugbank

Repurposing Hub list of drugs with functional annotations

data(repurp)
repurp

Gene targets from TTD

data(gene_targets)
gene_targets

Querying the data

The library also includes functions to match drugs by name across the different datasets, or to query a particular drug name among the CT interventions.

Clinical trials listing bortezomib as intervention

For example, below I show how to obtain a catalog of interventions in cancer-related clinical trials matched with the string bortezomib.

tbl <- find_intervention("bortezomib")

The function returns a list of interventions matched with the name bortezomib. Each intervention is associated with a unique clinical trial ID, title, status, date of registration, a detailed description of the study, and the number of enrolled subjects (either expected or actual) for r dplyr::n_distinct(tbl$id) clinical trials (out of r nrow(tbl) entries).

I use the function datatable from the package DT to show the results as HTML table.

require(DT)
DT::datatable(dplyr::select(tbl, -enrollment,-enrollment_type)
    , rownames = FALSE
    , filter = "top"
    , extensions = "Buttons"
    , plugins = "ellipsis"
    , options = list (
        dom = 'Bfrtip'
        , buttons =  c('copy', 'csv')
        , columnDefs = list(list(
                targets = c(2, 5)
                , render = JS("$.fn.dataTable.render.ellipsis( 125 )")
                )
            )
        )
    )