User: Valerie Obenchain

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Posts by Valerie Obenchain

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Answer: A: Data from ##SAMPLE lines in VCF?
... VariantAnnotation 1.27.6 and Rsamtools 1.33.6 have been updated to support VCFv4.3. I wanted to add some background to explain why we had the "META" DataFame in the first place. The meta-information lines in a VCF header are preceded by '##' and we can think of these key-value pairs as "simple" or ...
written 13 months ago by Valerie Obenchain6.7k
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Comment: C: Data from ##SAMPLE lines in VCF?
... Thanks for the report. The 'META' name clash is unfortunate. I'll work on a solution and should have something in they next couple of days. Valerie ...
written 13 months ago by Valerie Obenchain6.7k
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News: BioC 3.8 release schedule
... Hi all, The release of Bioconductor 3.8 will be on October 31:   https://www.bioconductor.org/developers/release-schedule/ Over the next weeks we'll announce key dates on the on bioc-devel@r-project.org mailing list. Thanks in advance for cleaning up packages and getting those last minute fixes ...
news bioconductor release written 14 months ago by Valerie Obenchain6.7k
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Answer: A: Trying to map nucleotide position from a transcript to genomic location
... Hi Vicky, I'm not sure why you think the results from mapFromTranscripts() are incorrect. I've used "Bcap29" as an example - Set up: snps <- GRanges("Bcap29", IRanges(1409, width=1)) library(org.Mm.eg.db) geneid <- select(org.Mm.eg.db, "Bcap29", "ENTREZID", "SYMBOL") txdb <- TxDb.Mmuscu ...
written 14 months ago by Valerie Obenchain6.7k
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Comment: C: getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was t
... Please update to a current version of R/Bioconductor (release is R 3.5 / Bioc 3.7). See this page for help: https://www.bioconductor.org/install/ If you still see the error after updating, post back and show your sessionInfo() again. Likely the error is triggered by specific ranges in myGranges. I ...
written 14 months ago by Valerie Obenchain6.7k
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Comment: C: Nearest genomic ranges and distances in circular ranges
... Hi, We've discussed this and it's not entirely clear what precede and follow mean for circular chromosomes. Should chromosome length be interpreted as the stop point in this case? For example, the current precede, follow have a select=c("first", "all") argument. What would be returned when select=a ...
written 15 months ago by Valerie Obenchain6.7k
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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 15 months ago by Valerie Obenchain6.7k
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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 16 months ago by Valerie Obenchain6.7k
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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 16 months ago by Valerie Obenchain6.7k
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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 16 months ago by Valerie Obenchain6.7k

Latest awards to Valerie Obenchain

Scholar 12 months ago, created an answer that has been accepted. For A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 18 months ago, created an answer that has been accepted. For A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
Popular Question 18 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 2.4 years ago, created an answer that has been accepted. For A: VariantAnnotation Installation Failure
Scholar 2.4 years ago, created an answer that has been accepted. For A: AnnotationHub: confusing pValue/qValue for (some) Roadmap records
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 2.4 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Bioconductor 3.5 is released
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Bioconductor Package Archives
Appreciated 2.4 years ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Appreciated 2.4 years ago, created a post with more than 5 votes. For Bioconductor 3.7 is released
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Popular Question 2.4 years ago, created a question with more than 1,000 views. For merging VCF files
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Integer overflow when summing an 'integer' Rle
Scholar 2.4 years ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 2.4 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 2.5 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 2.6 years ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 2.6 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 2.7 years ago, created a question with more than 1,000 views. For merging VCF files
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 2.8 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file

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