User: Tengfei Yin

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Tengfei Yin490
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Posts by Tengfei Yin

<prev • 47 results • page 1 of 5 • next >
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Answer: A: Bioconductor Digest, Vol 138, Issue 27
... Hey Laurent, Thanks a lot, just quickly go through it, this is very useful for me! I will look into it. cheers Tengfei On Wed, Aug 27, 2014 at 6:42 AM, Laurent Gatto wrote: > > Dear Anne and Tengfei, > > The mapping Pbase vignette [1] is an initial description of mapping protein & ...
written 5.2 years ago by Tengfei Yin490
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Comment: C: ggbio error: Objects of type OrganismDb not supported by autoplot
... Hey Jim, Thanks for your reply! Warning is fine, I removed the warning in the new version, it's just internally there is a "gap" in the type column as a byproduct; but in practice, you can you specify exons, cds, utr, the introns will be inferred, so no need for 'gap' type. Hey Georg So sorry for ...
written 5.2 years ago by Tengfei Yin490
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Answer: A: Positional Details with Features through UniProt.ws Ultimately to display as tra
... Hey Anne, So sorry for the late reply. Ideally, I should have some kind of mapper function in biovizBase to help map protein space to genomic space, so you don't have to do it yourself, but before I have that, a hack would be massage your protein domain data into a GRanges object, with domain fun ...
written 5.2 years ago by Tengfei Yin490
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Answer: A: plotIdeogram for non-human or mouse genome
... Hi Mark Sorry for the late reply, in short, there is a bug for cytoband parameters, I fixed in the released branch biovizBase 1.12.3, and ggbio 1.12.10. But "dm3" doesn't have gieStain value, that's another problem, you have to find it somewhere. Then manually assign the color like something below ...
written 5.2 years ago by Tengfei Yin490
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ggbio plot coverage adjusted for library size
... Hey James, So sorry for the late reply, in case I forget, you can also leave your question/feedback ingithub issues page backlog . I will work on those backlogs when I got time. Are you looking for a normalization cross samples for coverage? Unfortunately, it's not built-in yet. But I am re-work ...
coverage normalization written 5.2 years ago by Tengfei Yin490
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autoplot() in ggbio package for txdb object
... Hi Rebecca, So sorry for the late reply, in case I forget next time, please feel free to leave your question/feedback in github issues page backlog . I will work on those issues when I got time. For you question, yes, I just confirmed this is a bug in biovizBase/ggbio package for exons with no cds ...
ggbio written 5.2 years ago by Tengfei Yin490
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Comment: C: GenomicRanges seqlengths problem
... Glad that it works :) btw, if you use seqlevels to control how many chromosome shown in the circular view, make sure every track data, have exactly the same seqlevels and seqlengths, order matters too, I don't have any validation now for different tracks ... I will add one later. cheers On Sat, ...
written 5.5 years ago by Tengfei Yin490
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Comment: C: GenomicRanges seqlengths problem
... Hi Agnieszka, it's not really a ggbio related question, but would you mind try seqlevels(snps) <- names(seqlens) # then seqlengths(snps) <- seqlens to see if that solved your problem. cheers Tengfei On Sat, May 3, 2014 at 6:32 PM, Miss Agnieszka Aleksandra Golicz < agnieszka.golicz@ ...
written 5.5 years ago by Tengfei Yin490
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Answer: A: ggbio 1.12.0 autoplot() with txdb example is broken
... Hi Leo, Thanks for reporting the bugs, yes, this is a perfect time to report, if you read a new updated vignette (still keep updating it ...) in 1.12.3 http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst /doc/ggbio.pdf You will notice section 'add gene model' changed, it support ...
written 5.6 years ago by Tengfei Yin490
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Comment: C: ggbio 1.12.0 autoplot() with txdb example is broken
... it's good it's building, but it's very weird that it works, because I simply removed eval = TRUE for that chunk which is default. I came across some really weird *bug* in knitr which I try to reproduce with a minimal example, if you look closely, I put three blank code chunk at the front to avoid th ...
written 5.6 years ago by Tengfei Yin490

Latest awards to Tengfei Yin

Scholar 5.2 years ago, created an answer that has been accepted. For A: ggbio 1.12.0 autoplot() with txdb example is broken

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