Admin: Marcel Ramos

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Marcel Ramos ♦♦ 90
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90
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United States
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4 days, 1 hour ago
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3 years ago
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Posts by Marcel Ramos

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Inconsistent Warning: GRanges out of bounds
... Hi znl207, In order for anyone to provide assistance, please post a fully reproducible and minimal example of the issue. What I see from the output, it doesn't look like an error but more of a warning. It could be related to a number of issues including the integrity of the data. One option you coul ...
written 9 days ago by Marcel Ramos ♦♦ 90
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Answer: A: Error when subsetting a RaggedExperiment by GenomicRanges
... Hi Carlos, Thank you for your report. This is indeed a bug in the subsetByOverlaps,RaggedExperiment,Vector-method. This was fixed in version 1.2.4 in release and 1.3.7  in devel. Regards, Marcel ...
written 9 weeks ago by Marcel Ramos ♦♦ 90
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Answer: A: Error when prepare the TCGAdata
... Hi Michael Wang, This seems to be a memory issue. Methylation data is quite large and may exhaust your memory resources when trying to merge the various files that you've downloaded. The total size of the files is ~10.8 Gb. Downloading data for project TCGA-LUAD GDCdownload will download 507 files ...
written 11 weeks ago by Marcel Ramos ♦♦ 90
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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 3 months ago by Marcel Ramos ♦♦ 90
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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 3 months ago by Marcel Ramos ♦♦ 90
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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 3 months ago by Marcel Ramos ♦♦ 90
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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 3 months ago by Marcel Ramos ♦♦ 90
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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 5 months ago by Marcel Ramos ♦♦ 90
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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 5 months ago by Marcel Ramos ♦♦ 90
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Comment: C: Classes and methods for working with segmented copy number data
... Update: RaggedExperiment is now in Bioconductor devel! ...
written 10 months ago by Marcel Ramos ♦♦ 90

Latest awards to Marcel Ramos

Scholar 10 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data
Scholar 10 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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