new Parameter[] {
new Parameter("filename", preprocess.getURL(0).toString())
});
The last statements in the application download the preprocessed data and load it into a matrix for further analysis:
String downloadDirName=String.valueOf(preprocess.getJobNumber());
// download result files
File[] outputFiles = preprocess.downloadFiles(downloadDirName);
// load data into matrix for further manipulation
ExpressionData expressionData
=
IOUtil.readExpressionData(outputFiles[0].getPath());
}
}
You can combine GenePattern analyses with any capabilities that the Java environment has to offer. Use Java's 2-D
and 3-D graphics libraries to create graphic output, or summarize and report on the data using your own code. The
basic idea to remember is that GenePattern tasks create result files and those files are available to the Java
application for processing.
For a list of the GenePattern modules, with links to their documentation, see the
Modules page. To have GenePattern
generate the Java code required to run a task, build a pipeline that contains the desired task and then, in the
Pipelines pane of the GenePattern Web Client home page, use the Download Pipeline Code field to generate the
Java code for that pipeline.
Using LSIDs from Java
As of version 1.3 of the GenePattern server, Life Science Identifiers (LSIDs) can be used instead of task names to
identify tasks for GenePattern to run. An LSID may be submitted in place of the task name in the methods
runAnalysis and runVisualizer. When an LSID is provided that does not include a version, the latest
available version of the task identified by the LSID will be used. If a task name is supplied, the latest version of the
task with the nearest authority is selected. The nearest authority is the first match in the sequence: local authority,
Broad authority, other authority. For more information about LSIDs, see Understanding Version Numbers in the
GenePattern Java Client Guide.
Using GenePattern from MATLAB
Using MATLAB as a GenePattern client allows you to run GenePattern tasks and to manipulate and visualize the
results in a powerful, commercial technical computing application that works on most major platforms. Using
GenePattern allows you to invoke methods written in many other languages without having to worry about how to
launch them. This section describes how you can use the GenePattern MATLAB library to run GenePattern analyses:
●
Getting Started in MATLAB
● GenePattern MATLAB Library
●
Running a Program
●
Using LSIDs from MATLAB
Getting Started in MATLAB
Resources and documentation for MATLAB are available at http://www.mathworks.com/.
GenePattern MATLAB Library
The GenePattern MATLAB library allows you to invoke a GenePattern task as if it were a local MATLAB function
running on your client and to get back from the task a list of result files. A zip file containing the MATLAB library is
available on your GenePattern server.
To download the GenePattern MATLAB library to your computer:
1. Start the GenePattern Web Client.
18
Manymanuals.com
Manymanuals.de
Manymanuals.fr
Manymanuals.it
Manymanuals.pl
Manymanuals.cz
Manymanuals.es
Manymanuals-pt.com
Commenti su questo manuale