Admin: Valerie Obenchain
Valerie Obenchain ♦♦ 6.6k
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Posts by Valerie Obenchain
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... FYI this does not look related to the server updates I mentioned in response to this thread: https://stat.ethz.ch/pipermail/bioc-devel/2018-August/013896.html. I don't think my response has posted to bioc-devel yet but I wanted to close the loop here.
Valerie
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written 5 days ago by
Valerie Obenchain ♦♦ 6.6k
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... Hi Adrian,
Thanks for the clear example. It looks like precede(), follow() and the nearest() family don't support circular chromosomes. This is was probably my oversight when these were implemented and it will be fixed soon.
I'm editing my answer because the helpers I suggested won't work on all s ...
written 4 weeks ago by
Valerie Obenchain ♦♦ 6.6k
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... Hi,
I think you've identified a bug in motifbreakR. The maintainer should import info() from VariantAnnotation (currently they only import readVcf()).
The reason you see this error but the example on ?snps.from.file runs smoothly is because you are hitting a different conditional in the function. ...
written 6 weeks ago by
Valerie Obenchain ♦♦ 6.6k
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...
If the rsnumbers are in 'vcf_mod' you can map back to them with the QUERYID column in the output of locateVariants().
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written 6 weeks ago by
Valerie Obenchain ♦♦ 6.6k
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... Hi,
If the rsnumbers are the ID column of the VCF file they should be the rownames in the readVcf() output. This (which you may already know) is described in the ?readVcf man page:
rowRanges: The CHROM, POS, ID and REF fields are used to create a
‘GRanges’ object. Ranges are create ...
written 6 weeks ago by
Valerie Obenchain ♦♦ 6.6k
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Answer:
A: nearest without overlapping
... You could filter out the overlapping ranges before calling distanceToNearest():
> query <- GRanges("chr1", IRanges(5, width=6))
> subject <- GRanges("chr1", IRanges(start=c(15, 10, 20), width=5))
> overlaps <- subjectHits(findOverlaps(query, subject))
> distanceToNearest(query ...
written 7 weeks ago by
Valerie Obenchain ♦♦ 6.6k
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... Each version of Bioconductor is designed to work with an associated set of packages. For example the current release version of Bioconductor is 3.7 and the devel version is 3.8 (both use R 3.5). You can see the package versions associated with each on the build reports:
https://www.bioconductor.org ...
written 7 weeks ago by
Valerie Obenchain ♦♦ 6.6k
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Answer:
A: cram for new chips
... Hi,
Yes, you can provide your own annotation package for this chip. I'm not familiar with these data but with some help from a colleague (thanks Jim!) it sounds like they're similar to the infinium chip packages
https://www.bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethyla ...
written 7 weeks ago by
Valerie Obenchain ♦♦ 6.6k
0
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... Hi,
elementLengths() was deprecated some time ago (2016 I think) and replaced with elementNROWS(). The generic is in the S4Vectors package.
The current Bioconductor release and devel use R 3.5. S4Vectors is at version 0.18.3 in release and 0.19.14, you can see the most current versions on the buil ...
written 8 weeks ago by
Valerie Obenchain ♦♦ 6.6k
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... You can use filterVcf to remove rows from a vcf file that meet certain criteria. (The function does not filter by sample/column.)
From the ?filterVcf man page:
There are up to two passes. In the first pass, unparsed lines are passed to \code{prefilters} for filtering, e.g., searching for a fixed c ...
written 3 months ago by
Valerie Obenchain ♦♦ 6.6k
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For A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
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For A: about collapsed and expanded vcf file
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