MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Scaricare il pdf (Pagina 20)

Alternatively, to get the parameters with their default values filled in, use the

getMethodParameters function of

the

GenePatternServer object. This returns a MATLAB structure with named elements for each parameter,

filled in with the default value if one exists. After filling in the missing parameters and overriding defaults if desired,

this structure can then be passed on to the runAnalysis method.

% display the available GenePattern modules

params2 = getMethodParameters(gp, 'TransposeDataset')

params2.input_filename='http://www.broad.mit.edu/mpr/publications/projects/Leu

kemia/ALL_vs_AML_train_set_38_sorted.res'

% transpose the dataset

transposeResult = gp.TransposeDataset(params2)

The GenePattern MATLAB library also has convenience methods to read and write GenePattern files (such as res,

gct, and odf files). Even if you choose not to look in the library, you can extend the techniques shown above to

implement your own analyses.

Using LSIDs from MATLAB

As of GenePattern version 1.3, you can use Life Science Identifiers (LSIDs) to identify a task when executing

GenePattern code in MATLAB. An LSID may be submitted in place of the task name to

getMethodParameters

runAnalysis. When providing an LSID to a method in addition to a task name, the LSID alone is used to

determine what task to run. 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. For more information about LSIDs, see

Understanding Version Numbers

in the GenePattern Java Client Guide.

% Example using LSIDs from MATLAB

params = getMethodParameters(gp,

'urn:lsid::broad.mit.edu:cancer.software.genepattern.

module.analysis:00026:0'); params.output_file_name = 'transposed.out'

params.input_filename='http://www.broad.mit.edu/mpr/publications/projects/Leuk

emia/ALL_vs_AML_train_set_38_sorted.res'

% transpose the dataset

transposeResult = runAnalysis(gp,

'urn:lsid::broad.mit.edu:cancer.software.genepattern.module.analysis:00026:0',

params)

Using GenePattern from R

Using R as a GenePattern client allows you to run GenePattern tasks and to manipulate and visualize the results in a

powerful, free statistical desktop package 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 or whether you

are passing incorrect parameters. This section describes how you can use the GenePattern R library to run

GenePattern analyses:

●

Getting Started in R

●

Accessing GenePattern from R

●

Running a Program

●

Using LSIDs from R

Getting Started in R

If you are not familiar with R, see the following resources on the www.r-project.org website:

●

An Introduction to R (PDF, approx. 100 pages, 650kB), based on the former "Notes on R", gives an introduction

to the language and how to use R for doing statistical analysis and graphics.

● A draft of

the R language definition (PDF, approx. 60 pages, 400kB) documents the language; that is, the objects

that it works on, and the details of the expression evaluation process, which are useful to know when

programming R functions.

●

Writing R Extensions (PDF, approx. 85 pages, 500kB) covers how to create your own packages, write R help

files, and the foreign language (C, C++, Fortran, ...) interfaces.

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