User: rcavalca

gravatar for rcavalca
rcavalca40
Reputation:
40
Status:
New User
Location:
United States
Twitter:
rcavalcante
Last seen:
5 days, 19 hours ago
Joined:
2 years, 6 months ago
Email:
r*******@umich.edu

Posts by rcavalca

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Chipenrich expected fit line
... Unfortunately the graphic is not editable (for example if we were to use ggplot2 and return the plot object), so you'd need to fiddle the source code and alter it to your liking. ...
written 9 days ago by rcavalca40
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Answer: A: Unable to find an inherited method for function distanceToNearest for signature
... Hello, Unfortunately, I'm not able to reproduce this error. Can you please post yours and maybe that'll help? I'm running R 3.4.1, chipenrich 2.0.1, and chipenrich.data 2.0.0. I'm not seeing errors with this on the Bioconductor build system, and peaks_E2F4 is used in the build process, so I'm a bit ...
written 9 days ago by rcavalca40
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Answer: A: Error while using champ.svd() function in subset of data
... Hello, I'm a colleague of the poster, but I figured I'd post my findings here in case anyone else has this issue. The problem turned out to be that one of the columns (Slide) in our phenotype data could be construed as numeric, and so in the block for(c in 1:topPCA) for(f in 1:ncol(Ph ...
written 7 weeks ago by rcavalca40
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Answer: A: Error with mappability argument
... Hi Ashley, Sorry for the delay in response, I was out of town. You're absolutely right. I should be coercing that parameter to a character before checking to see if it's a custom mappability file path that's given. I've fixed this in the devel version, and will similarly fix it in the release vers ...
written 6 months ago by rcavalca40
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Answer: A: chipenrich mm10 error
... Yikes! Thank you for pointing this out! I just pushed a patch (v1.12.1) to the release branch of Bioconductor. You can wait for it to work through the build system, or you can install the version with devtools::install_github('Bioconductor-mirror/chipenrich@release-3.4'). Thanks for using chipenri ...
written 8 months ago by rcavalca40
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Answer: A: find intersections of genomic regions with built-in genomic annotations for S.Ce
... Hi Viviane, Thanks for using annotatr. At the moment you need to provide S. Cerevisiae annotations as custom annotations with the read_annotations() function. I am currently working on a more general function to convert any GRanges resource in the AnnotationHub  package into an annotation for use i ...
written 9 months ago by rcavalca40
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Comment: C: find intersections of genomic regions with built-in genomic annotations for S.Ce
... Hi Viviane, Thanks for using annotatr. At the moment you need to provide S. Cerevisiae annotations as custom annotations with the read_annotations() function. I am currently working on a more general function to convert any GRanges resource in the AnnotationHub  package into an annotation for use i ...
written 9 months ago by rcavalca40
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Answer: A: annotatr GRanges Error
... Hello, I wanted to follow up to let you know GenomeInfoDb has been updated to 1.10.3 on the release branch and 1.11.9 on the devel branch. The update fixes the issue causing the error in both. Since they haven't made their way through the Bioconductor build system, I installed the release version w ...
written 9 months ago by rcavalca40
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Answer: A: annotatr GRanges Error
... Hello, Thanks for using annotatr. It looks like there is a GRanges warning that some ranges are out of the chromosome bounds. This is normal because some of the annotations extend regions and are then trimmed. The error looks to be related to the lncRNA resource. > Error in file(file, "rt") : c ...
written 9 months ago by rcavalca40
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Comment: C: Annotatr package not loading certain features
... Hello, Sorry for the very delayed response, despite your use of the annotatr tag, I didn't get a notification about this message. Given Valerie's response (thanks), I would guess it was a temporary blip in access to AnnotationHub. I have experienced this before, and just waited it out. Thanks for ...
written 11 months ago by rcavalca40

Latest awards to rcavalca

Scholar 8 months ago, created an answer that has been accepted. For A: chipenrich mm10 error

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