User: rcavalca

gravatar for rcavalca
rcavalca90
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90
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Trusted
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United States
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rcavalcante
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1 day, 22 hours ago
Joined:
2 years, 9 months ago
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r*******@umich.edu

Posts by rcavalca

<prev • 20 results • page 1 of 2 • next >
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Answer: A: Unexpected results from annotatr
... Hello, The annotations in annotatr include all the transcripts for a particular gene. In this case Got1 has an annotation for knownGene transcript uc008hoj.1 as 1to5kb upstream of a TSS, and it overlaps an intron that transcript uc012bmb.1 has. And in this case, your input region intersects both of ...
written 2 days ago by rcavalca90
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Answer: A: 'fill_order' in annotatr
... Hello, "fill_order" to the ordering of the bars in the bar chart, and also the legend. annotatr doesn't do a prioritization, really. It reports all the intersections of a region with annotations. So if a region is in both a UTR and CDS, it will count towards each of those categories in the bar char ...
written 3 days ago by rcavalca90
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Answer: A: How can I use Annotatr on CDS?
... Hi, thanks for using annotatr. The CDS can be used with mm10_genes_cds. For a visual idea of where that falls: http://bioconductor.org/packages/release/bioc/vignettes/annotatr/inst/doc/annotatr-vignette.html#genic-annotations Hope that answers your question. ...
written 9 days ago by rcavalca90
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Comment: C: Unable to find an inherited method for function distanceToNearest for signature
... This is truly bizarre. I'm sorry, but I'm not sure what to do... ...
written 12 weeks ago by rcavalca90
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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 3 months ago by rcavalca90
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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 3 months ago by rcavalca90
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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 4 months ago by rcavalca90
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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 9 months ago by rcavalca90
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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 11 months ago by rcavalca90
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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 12 months ago by rcavalca90

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Scholar 11 months ago, created an answer that has been accepted. For A: chipenrich mm10 error

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