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Run Gene Pattern (GenePattern) from R

Simple question, but one I have struggled with due to weak R skills.

I have set up a local instance of GenePattern with no issues i.e. the GUI works fine. In addition, I can follow this tutorial that links R and Gene Pattern with no problems:

http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/programmers/sections/gp_r

My problem arises when I go off and try to run other modules with my own code. Would someone be willing to share some example R code that can call a GenePattern module? I just can't find any other examples (specific or generic) on the web that will help me teach myself.

Thanks.

-Brian Muchmore

r genepattern
• 5,995 views • link
updated by Ram Ram • written by bmuchmore • bmuchmore

1 answer

Hi Brian,

If you've already read the R Programming Guide section, one other thing you can do is to generate the R code to call the module you've created. You will then be able to paste it into your R program to run the module.

To do this, log in to your GenePattern server and select the module you would like to call through R. On the right-hand side of the module's title you will see a gear icon. Click this icon and select "R code". You will then see a line of R code that you can use to call that module, when you substitute your desired parameters. (This assumes you have also included the GenePattern R library and set up your R script as described in the programmer's guide.)

If this doesn't work, can you paste an example of the call you are making that isn't working?

Best,
Michael

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updated by Ram Ram • written by Michael Reich • Michael Reich

Thanks for the input Michael. I tried what you suggested and it worked without a hitch. I did the same thing yesterday, but for whatever reason it was not working. What I give real credit to, however, is RKWard, which allowed me to investigate the various functions in the GenePattern library, so I could understand what all the calls were doing. Previously, I had not found any documentation for that. Thanks again for your input.

-Brian

• 0 views • link
updated by Ram Ram • written by bmuchmore • bmuchmore

Thanks Brian - glad it's working, and thanks for the tip about RKWard!

Best,
Michael

• 0 views • link
updated by Ram Ram • written by Michael Reich • Michael Reich

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