Question: Retrieving clinical trial data using R program
0
gravatar for niveditaj20
5.5 years ago by
niveditaj2050
niveditaj2050 wrote:

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?

eg. 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, Carboplatin, and Pemetrexed Disodium in Treating Patients With Stage IV Non-Small Cell Lung Cancer

Active, not recruiting

Adenocarcinoma of the Lung; Bronchoalveolar Cell Lung Cancer; Large Cell Lung Cancer; Recurrent Non-small Cell Lung Cancer; Stage IV Non-small Cell Lung Cancer

Drug: PI3K inhibitor BKM120; Drug: pemetrexed disodium; Drug: carboplatin; Other: laboratory biomarker analysis; Other: pharmacological study; Procedure: quality-of-life assessment

May 5, 2015

0.99273

NCT01540253

http://ClinicalTrials.gov/show/NCT01540253

PI3K Inhibitor BKM120 and Docetaxel in Treating Patients With Advanced Solid Tumor That is Locally Advanced, Cannot Be Removed By Surgery, or Metastatic

Active, not recruiting

Unspecified Adult Solid Tumor, Protocol Specific

Drug: PI3K inhibitor BKM120; Drug: docetaxel; Other: pharmacological study; Other: questionnaire administration; Other: laboratory biomarker analysis

April 23, 2015

Kindly need help.

R gene • 1.5k views
ADD COMMENTlink modified 5.5 years ago by Giovanni M Dall'Olio27k • written 5.5 years ago by niveditaj2050
3

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

ADD REPLYlink written 5.5 years ago by Sean Davis26k

Dear Davis,

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

 

ADD REPLYlink written 5.5 years ago by niveditaj2050
2

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

ADD REPLYlink written 5.5 years ago by Sean Davis26k
4
gravatar for Selenocysteine
5.5 years ago by
Dublin, Ireland
Selenocysteine600 wrote:

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)

 

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Selenocysteine600
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