User: rcavalca

gravatar for rcavalca
rcavalca110
Reputation:
110
Status:
Trusted
Location:
United States
Twitter:
rcavalcante
Last seen:
4 days, 17 hours ago
Joined:
3 years ago
Email:
r*******@umich.edu

Posts by rcavalca

<prev • 24 results • page 1 of 3 • next >
1
vote
1
answer
42
views
1
answer
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 days ago by rcavalca110 • updated 5 days ago by emmascottgm0
0
votes
1
answers
57
views
1
answers
Comment: C: Strange error in bsseq when trying to assign seqinfo
... Sounds good, thanks for the fix! ...
written 8 days ago by rcavalca110
7
votes
1
answer
57
views
1
answer
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 9 days ago by rcavalca110 • updated 9 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
114
views
1
answers
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 12 weeks ago by rcavalca110
0
votes
1
answers
89
views
1
answers
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 3 months ago by rcavalca110
0
votes
1
answers
120
views
1
answers
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 months ago by rcavalca110
0
votes
1
answers
108
views
1
answers
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 3 months ago by rcavalca110
0
votes
1
answers
228
views
1
answers
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 5 months ago by rcavalca110
0
votes
1
answers
134
views
1
answers
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 6 months ago by rcavalca110
0
votes
1
answers
228
views
1
answers
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 6 months ago by rcavalca110

Latest awards to rcavalca

Scholar 12 months ago, created an answer that has been accepted. For A: chipenrich mm10 error
Scholar 12 months ago, created an answer that has been accepted. For A: Chipenrich expected fit line
Scholar 12 months ago, created an answer that has been accepted. For A: 'fill_order' in annotatr
Scholar 12 months ago, created an answer that has been accepted. For A: Unexpected results from annotatr
Scholar 14 months ago, created an answer that has been accepted. For A: chipenrich mm10 error

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 262 users visited in the last hour