Admin: Marcel Ramos

gravatar for Marcel Ramos
Marcel Ramos ♦♦ 80
Reputation:
80
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Location:
United States
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2 days, 4 hours ago
Joined:
2 years, 9 months ago
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m***********@roswellpark.org

Posts by Marcel Ramos

<prev • 22 results • page 1 of 3 • next >
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Comment: C: GenomicRanges_RaggedExperiment Error in as background, class mcol no method or d
... Updates: This has been fixed in `1.2.3` in release and `1.3.5` in devel.  Marcel ...
written 2 days ago by Marcel Ramos ♦♦ 80
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Answer: A: GenomicRanges_RaggedExperiment Error in as background, class mcol no method or d
... Hi Taran,  Apologies for the late response. I have looked at the issue and we're working on a fix.  The reason you're getting an error in that call is that you are introducing an "score" column of type `factor`.  The quick fix for this issue is to coerce the "score" column to character and rerun th ...
written 2 days ago by Marcel Ramos ♦♦ 80
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Comment: C: GenomicRanges_RaggedExperiment Error in as background, class mcol no method or d
... Hi Taran,  Thank you for your report. I wasn't able to get to it yesterday. I will have a look at it today.  Regards, Marcel ...
written 5 days ago by Marcel Ramos ♦♦ 80
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Comment: C: Calulation of ka/ks (dn/ds) using sliding windows
... Hi Emilio, It is always more helpful to provide a reproducible example snippet of the code and data you currently have and a text representation of the result that you want to achieve. This way those who view your question are more likely to provide a response.  I would also discourage the use of ...
written 22 days ago by Marcel Ramos ♦♦ 80
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[RCircos] Examples flagged as not run
... Dear Henry, I've tried to run the examples under the RCircos.Reset.Core.Components {RCircos} page. There are a couple of typos in the examples (in asterisks below): rows <- which(ideo$BandColor=="red"**)** RCircos.Reset.Plot.Param**e**ters(params) Could you also please remove the ## Not ru ...
bug rcircos written 9 weeks ago by Marcel Ramos ♦♦ 80
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Answer: A: converting a GRangesList object with different lengths into a data frame
... Hi Assa Yeroslaviz, If you collapse into a single data.frame, each row will represent a different genomic location. You may not want this. Nevertheless, if you do want to go ahead and do this, you can try this: # Take all the score values scoreList <- lapply(tiles.list, function(x) mcols(x)) # I ...
written 10 weeks ago by Marcel Ramos ♦♦ 80
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Comment: C: Classes and methods for working with segmented copy number data
... Update: RaggedExperiment is now in Bioconductor devel! ...
written 7 months ago by Marcel Ramos ♦♦ 80
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Answer: A: Classes and methods for working with segmented copy number data
... Update: Please see the latest package submission (RaggedExperiment) for this type of data. https://github.com/Bioconductor/Contributions/issues/339 and the GitHub version of the package https://github.com/Bioconductor/RaggedExperiment/    Sincerely,  Marcel ...
written 7 months ago by Marcel Ramos ♦♦ 80
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Answer: A: Sorting the VIEW index in ascending/descending order
... Hi Rob,  I would really discourage the use of View for anything other than a matrix or data.frame.  The class should have a good enough show method so that you wouldn't need to use View.    Regards, Marcel  ...
written 7 months ago by Marcel Ramos ♦♦ 80
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Answer: A: seqlm installation error
... Hi niutster,  A couple of points:  If you are using Bioconductor, the recommended way to install a github package is `BiocInstaller::biocLite("raivokolde/seqlm")`.  Since this package is not part of Bioconductor, we can't provide support with any issues that may arise from it.    I tried to ins ...
written 9 months ago by Marcel Ramos ♦♦ 80

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Scholar 7 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data
Scholar 7 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data

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