Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 6.6k
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Posts by Valerie Obenchain

<prev • 816 results • page 1 of 82 • next >
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Comment: C: ExperimentHub wackiness (which breaks packages that depend upon experimentHub-pr
... 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 ...
written 5 days ago by Valerie Obenchain ♦♦ 6.6k
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Answer: A: Nearest genomic ranges and distances in circular ranges
... 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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Comment: C: Error with R package motifbreakR while trying to read a vcf file with snps.from.
... 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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Comment: C: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
... If the rsnumbers are in 'vcf_mod' you can map back to them with the QUERYID column in the output of locateVariants(). ...
written 6 weeks ago by Valerie Obenchain ♦♦ 6.6k
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Answer: A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
... 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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Answer: A: Error: invalid class "VRanges" object
... 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
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Answer: A: Error with R package motifbreakR while trying to read a vcf file with snps.from.
... 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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Answer: A: filtering a VCF file based on genotype
... 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

Latest awards to Valerie Obenchain

Scholar 3 months ago, created an answer that has been accepted. For A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
Popular Question 3 months ago, created a question with more than 1,000 views. For merging VCF files
Popular Question 13 months ago, created a question with more than 1,000 views. For Integer overflow when summing an 'integer' Rle
Popular Question 13 months ago, created a question with more than 1,000 views. For Bioconductor 3.5 is released
Scholar 13 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Appreciated 13 months ago, created a post with more than 5 votes. For Bioconductor 3.7 is released
Scholar 13 months ago, created an answer that has been accepted. For A: AnnotationHub: confusing pValue/qValue for (some) Roadmap records
Scholar 13 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Popular Question 13 months ago, created a question with more than 1,000 views. For Bioconductor Package Archives
Appreciated 13 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 13 months ago, created an answer that has been accepted. For A: VariantAnnotation Installation Failure
Popular Question 13 months ago, created a question with more than 1,000 views. For merging VCF files
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 14 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 14 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 15 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 16 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 17 months ago, created a question with more than 1,000 views. For merging VCF files
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 19 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 2.3 years ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 2.3 years ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)

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