User: mscherer

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mscherer10
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Posts by mscherer

<prev • 4 results • page 1 of 1 • next >
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Comment: C: RnBeads set ghost script environment variable
... Dear Kathrin, You'll also have to add the path to the Ghostscript executable to your ```PATH``` environment variable as described in the RnBeads FAQ under [rnbeads.org/faq.html][1]. Under Windows 7, for instance, you can specify that in the Control Panel in the Systems properties. I hope that help ...
written 5 weeks ago by mscherer10
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Answer: A: Obtaining annotated results from rnbeads
... Dear Mark, That is easily solved. The obtained results have the same dimension as the methylation and annotation matrices stored in the ```rnb.set``` object. You can access this information using: anno.genes <- annotation(rnb.set,"genes") anno.proms <- annotation(rnb.set,"promoters") ...
written 6 months ago by mscherer10
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Comment: C: Trouble creating an RnBeads annotation for rn6 rat genome build
... Hey Richard, The maxSNPs parameter is used as the maximum batch size. So if you have more SNPs than this number, RnBeads suggests to use a compute cluster for that. This is the case you are in. RnBeads automatically creates a script that you can use for job scheduling with PBS. In your case, it is ...
written 10 months ago by mscherer10
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Answer: A: Trouble creating an RnBeads annotation for rn6 rat genome build
... Hey Richard, I just had a look into the code for the annotation creator and found the following function definition: createAnnotationPackage <- function(assembly,dest=getwd(),maxSNPs=500000L,cleanUp=TRUE) The parameter *maxSNPs* accounts for the maximal number of SNPs allowed in any given ...
written 10 months ago by mscherer10

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