MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Scaricare il pdf (Pagina 21)

●

R Data Import/Export (PDF, approx. 35 pages, 270kB) describes the import and export facilities available either

in R itself or via packages which are available from CRAN.

●

R Installation and Administration (PDF, approx. 30 pages, 200kB).

●

The R Reference Index (PDF, approx. 2200 pages, 12MB) contains all help files of the R standard and

recommended packages in printable form.

Accessing GenePattern from R

The GenePattern R library allows you to invoke a GenePattern task as if it were a local R method running on your

client and to get back from the task a list of result files. The R library is available on your GenePattern server in both

Windows (zip) and Unix (tar.gz) formats.

To download the R library to your computer:

1. Start the GenePattern Web Client.

2. Under Programming Libraries in the right column, click the

zip or tar.gz link for the R library.

3. After downloading the zip file, extract it into your

R/library directory.

If you cannot add files to your

R/library directory (because it is a publicly-shared version and you do not

have appropriate privileges), you can load the GenePattern library by setting the environment variable

R_LIBS=

<GenePattern install directory>/R/library in your autoexec.bat, .cshrc,

.bashrc or other shell startup file. R will then load from its usual location, but will also search for and find the

GenePattern library.

Running a Program

This section explores a simple R program that runs a task, displays the resulting output, and loads it into an R matrix

for further analysis. The included code can be copied and pasted into your R client so that you can try it out, modify it,

and create your own solutions.

The first statements in the application initialize various settings, which you must do once in every application that

accesses GenePattern. You will need to customize the italicized GenePattern user name (typically, your e-mail

address). The

gpTasksAsFunctions method creates a function for each GenePattern task on the server, which

invokes the latest version of that task.

# Load GenePattern library

library(GenePattern)

defaultServer <- "cp409-6ac.domain.com:8080"

# The server will want to know whose tasks to provide

gpLogin("[email protected]");

# Ask the server to create R methods that proxy

# each of the installed tasks.

gpTasksAsFunctions();

Note: In GenePattern 2.0.2, the R programming environment does not handle HTTP redirects; therefore, you must

set the value of the defaultServer variable to the full host name of your GenePattern server, as shown above. To find

the host name of your GenePattern server, open the GenePattern Web Client and check the URL displayed in the

web browser window.

After initializing the required settings, the application runs the TransposeDataset task to transpose a dataset. This

example references the dataset using a publicly-accessible URL, but a filename would be equally valid. When you

call an R method, such as

TransposeDataset, the GenePattern library invokes the appropriate task on the

server, passing all of the input parameters and input files. Control returns to your application when the task

completes. (To run a task asynchronously, invoke the method in a separate thread.)

# input dataset for transpose operation

input.ds <-

"http://www.broad.mit.edu/mpr/publications/projects/Leukemia/ALL_vs_AML_train_

set_38_sorted.res";

# transpose the dataset

transpose.out <- TransposeDataset(input.filename=input.ds,

output.file.name="transposed");

1 2 ... 16 17 18 19 20 21 22

Commenti su questo manuale

Nessun commento

MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Pagina 21

Commenti su questo manuale