User: rcavalca

gravatar for rcavalca
rcavalca120
Reputation:
120
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United States
Twitter:
rcavalcante
Last seen:
5 months ago
Joined:
3 years, 5 months ago
Email:
r*******@umich.edu

Posts by rcavalca

<prev • 24 results • page 1 of 3 • next >
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Request to remove requirement for gr to have widths 1 in BSseq constructor
... Hi, I'm a big fan of bsseq because it is exactly the data structure I need for a package I maintain (methylSig) that tests for differential methylation (at CpGs and over regions). As of the Bioc 3.7 release it appears that a check in the BSseq constructor was added (I don't see a reference to it in ...
bsseq R package written 5 months ago by rcavalca120 • updated 5 months ago by emmascottgm0
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Comment: C: Strange error in bsseq when trying to assign seqinfo
... Sounds good, thanks for the fix! ...
written 5 months ago by rcavalca120
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Strange error in bsseq when trying to assign seqinfo
...   Hello, I'm having a strange issue in R 3.5.0 / Bioc 3.7 when trying to assign seqinfo to a bsseq object that I don't have in R 3.4.3 / Bioc 3.6. The particular error I get can be reproduced with the following code: # Do not load any libraries seqinfo_hg19 = GenomeInfoDb::Seqinfo(genome = 'hg19 ...
genomicranges bsseq genomeinfodb seqinfo written 5 months ago by rcavalca120 • updated 5 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: ENSEMBL database for annotatr
... Hello, Correct, annotatr uses the UCSC knownGenes database. If there was a TxDb package for hg19 that used ENSEMBL as its basis, it would be fairly easy to create the annotations, but I am not aware of such a TxDb package. As to your question about read_regions(), my understanding is that 1 is add ...
written 7 months ago by rcavalca120
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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 7 months ago by rcavalca120
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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 7 months ago by rcavalca120
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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 8 months ago by rcavalca120
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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 10 months ago by rcavalca120
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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 11 months ago by rcavalca120
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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 11 months ago by rcavalca120

Latest awards to rcavalca

Scholar 17 months ago, created an answer that has been accepted. For A: chipenrich mm10 error
Scholar 17 months ago, created an answer that has been accepted. For A: Chipenrich expected fit line
Scholar 17 months ago, created an answer that has been accepted. For A: 'fill_order' in annotatr
Scholar 17 months ago, created an answer that has been accepted. For A: Unexpected results from annotatr
Scholar 19 months ago, created an answer that has been accepted. For A: chipenrich mm10 error

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