Retrieving clinical trial data using R program

Question

[niveditaj20]

Hi,

Am new to programming and need your help on this:

I have a list of 800 genes/targets for which I need clinical trail study information. How to do it using R program?

e.g., I have done it for one target, but how can I get information on all the list I have at one go?

Code tried is as below:

clinicaltrials_search(query = "PI3K", count = 20)

and got the below output:

score    nct_id       url                                           title                          status.text             condition_summary                      intervention_summary                     last_changed
0.99384  NCT01723800  http://ClinicalTrials.gov/show/NCT01723800    PI3K Inhibitor BKM120,         Active, not recruiting  Adenocarcinoma of the Lung;            Drug: PI3K inhibitor BKM120;             May 5, 2015
                                                                    Carboplatin, and Pemetrexed                            Bronchoalveolar Cell Lung Cancer;      Drug: pemetrexed disodium;
                                                                    Disodium in Treating Patients                          Large Cell Lung Cancer;                Drug: carboplatin;
                                                                    With Stage IV Non-Small                                Recurrent Non-small Cell Lung Cancer;  Other: laboratory biomarker analysis;
                                                                    Cell Lung Cancer                                       Stage IV Non-small Cell                Other: pharmacological study;
                                                                                                                           Lung Cancer                            Procedure: quality-of-life assessment
0.99273  NCT01540253  http://ClinicalTrials.gov/show/NCT01540253    PI3K Inhibitor BKM120          Active, not recruiting  Unspecified Adult Solid Tumor,         Drug: PI3K inhibitor BKM120;             April 23, 2015
                                                                    and Docetaxel in                                       Protocol Specific                      Drug: docetaxel;
                                                                    Treating Patients                                                                             Other: pharmacological study;
                                                                    With Advanced Solid                                                                           Other: questionnaire administration;
                                                                    Tumor That is Locally                                                                         Other: laboratory biomarker analysis
                                                                    Advanced, Cannot Be
                                                                    Removed By Surgery,
                                                                    or Metastatic

Kindly need help.

[Sean Davis]

Is there any reason a loop over the genes would not suffice?

[niveditaj20]

Dear Davis,

I haven't tried looping yet. Kindly help me with it.

[Sean Davis]

Try using a "for" loop. You'll need to do a little reading to learn how to apply that to your situation.

Answer 1

[Selenocysteine]

Hi,

Following Sean's suggestion, I wrote you this piece of code.

Please note: in clinicaltrials_search, you set "count" to 20, so it only returns the 20 best matches for each gene. If you want to get more, change the value. :)

Edited

I just read that your gene list has 800 members... therefore it is better if you import if from a file. The following script will work with a txt file (called gene_list.txt), where all the gene identifiers are listed in the first column.

Code:

library(rclinicaltrials)

# Imports the gene list as a char vector
genes = as.character(read.table("gene_list.txt")[, 1])

# Gets the corresponding clinical trials
results = NULL
for(gene in genes){
  results = rbind(results, clinicaltrials_search(query = gene, count = 20))
}

print(results)