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download_expression.m

Download expression data for a given set of probe_ids.

 
function [samples,explevels] = download_expression(probe_ids, donor_ids)

Copyright 2013 Allen Institute for Brain Science Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

 

      		
    

    

      
        

          
        

        
Convert the probe ids into a comma-separated string.

      		
      
        
nprobes = numel(probe_ids);
if (nprobes > 1)
    probe_str = num2str(probe_ids','%d,');
    probe_str = probe_str(1:end-1);   
else
    probe_str = num2str(probe_ids','%d');
end

      		
    

    

      
        

          
        

        
Convert the donor ids into a comma-separated string.

      		
      
        
ndonors = numel(donor_ids);
if (ndonors > 1)
    donor_str = num2str(donor_ids','%d,');
    donor_str = donor_str(1:end-1);
else
    donor_str = num2str(donor_ids','%d');
end
      

      		
    

    

      
        

          
        

        
Make the request and parse the results as JSON.

      		
      
        
service = get_api_path();
request = '/query.json?criteria=service::human_microarray_expression';
probes = sprintf('[probes$in%s]',probe_str);
donors = sprintf('[donors$eq%s]',donor_str);
url = [service request probes donors];
disp(url);

str = urlread(url);
json = parse_json(str);

      		
    

    

      
        

          
        

        
Pull out the samples, probes, and expression levels from the results.


      		
      
        
samples = json.msg.samples;
nsamples = numel(samples);
probes = json.msg.probes;
explevels = zeros(nsamples,nprobes);
for i=1:nprobes
    explevels(:,i) = cellfun(@str2num, probes{i}.expression_level);
end